Sequence utilities

Collaboration diagram for Sequence utilities:

Classes
class	CDeflineGenerator
	Class for computing sequences' titles ("definitions"). More...
class	CDeflineGenerator::CLowQualityTextFsm
	exception fields More...
class	CGetOverlappingFeaturesPlugin
class	CSeqIdFromHandleException
class	CFastaOstream
	FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp> More...
struct	CFastaOstream::SGapModText
	This indicates the text of the modifiers of a gap. More...
class	CCdregion_translate
	Public interface for coding region translation function Uses CTrans_table in <objects/seqfeat/Genetic_code_table.hpp> for rapid translation from a given genetic code, allowing all of the iupac nucleotide ambiguity characters. More...
class	CSeqTranslator
struct	SRelLoc
	Location relative to a base Seq-loc: one (usually) or more ranges of offsets. More...
class	CSeqSearch
	============================================================================// Sequence Search // ============================================================================// More...
class	CSeqSearch::CPatternInfo
	Holds information associated with a pattern, such as the name of the restriction enzyme, location of cut site etc. More...
class	CSeqSearch::IClient
	Client interface: ================== A class that uses the SeqSearch facility should implement the Client interface and register itself with the search utility to be notified of matches detection. More...
class	CSequenceAmbigTrimmer
	This trims ambiguous bases from the start and/or end of sequences, using customizable rules. More...
struct	CSequenceAmbigTrimmer::STrimRule
	For example, if bases_to_check is 10 and max_bases_allowed_to_be_ambig is 5, then on each iteration we check the 10 terminal bases and trim off those 10 if there are more than 5 ambiguous bases there. More...
struct	CSequenceAmbigTrimmer::SAmbigCount
	This holds the output of x_CountAmbigInRange. More...
class	CBioseqGaps_CI
	This iterates over the runs of Ns of each sequence. More...
struct	CBioseqGaps_CI::Params
	The params that control the behavior of CBioseqGaps_CI. More...
struct	CBioseqGaps_CI::SCurrentGapInfo
	This indicates the state of the iterator right now. More...

Typedefs
typedef int	CDeflineGenerator::TUserFlags
	Binary "OR" of EUserFlags. More...
typedef long	CFastaOstream::TFlags
	binary OR of EFlags More...
typedef AutoPtr< char, ArrayDeleter< char > >	CFastaOstream::TCharBuf
typedef map< TSeqPos, int >	CFastaOstream::TMSMap
typedef int	CSeqTranslator::TTranslationFlags
typedef int	SRelLoc::TFlags
	binary OR of EFlags More...
typedef CSeq_interval	SRelLoc::TRange
	For relative ranges (ONLY), id is irrelevant and normally unset. More...
typedef vector< CRef< TRange > >	SRelLoc::TRanges
typedef CPatternInfo	CSeqSearch::TPatternInfo
typedef CSeqSearch::TPatternInfo	CSeqSearch::IClient::TPatternInfo
typedef unsigned int	CSeqSearch::TSearchFlags
	binary OR of ESearchFlag More...
typedef int	CSequenceAmbigTrimmer::TFlags
typedef vector< STrimRule >	CSequenceAmbigTrimmer::TTrimRuleVec
	Multiple STrimRules are allowed, which are applied from smallest bases_to_check to largest bases_to_check, and redundant rules are automatically removed. More...
typedef bool	CSequenceAmbigTrimmer::TAmbigLookupTable[26]

Enumerations
enum	CDeflineGenerator::EUserFlags {   CDeflineGenerator::fIgnoreExisting = 1 << 0 , CDeflineGenerator::fAllProteinNames = 1 << 1 , CDeflineGenerator::fLocalAnnotsOnly = 1 << 2 , CDeflineGenerator::fNoExpensiveOps = fLocalAnnotsOnly ,   CDeflineGenerator::fGpipeMode = 1 << 3 , CDeflineGenerator::fOmitTaxonomicName = 1 << 4 , CDeflineGenerator::fDevMode = 1 << 5 , CDeflineGenerator::fShowModifiers = 1 << 6 ,   CDeflineGenerator::fUseAutoDef = 1 << 7 , CDeflineGenerator::fFastaFormat = 1 << 8 , CDeflineGenerator::fDoNotUseAutoDef = 1 << 9 }
	User-settable flags for tuning behavior. More...
enum	CSeqIdFromHandleException::EErrCode { CSeqIdFromHandleException::eNoSynonyms , CSeqIdFromHandleException::eRequestedIdNotFound }
enum	CFastaOstream::EFlags : long {   CFastaOstream::fAssembleParts = 1 << 0 , CFastaOstream::fInstantiateGaps = 1 << 1 , CFastaOstream::fSuppressRange = 1 << 2 , CFastaOstream::fReverseStrand = 1 << 3 ,   CFastaOstream::fKeepGTSigns = 1 << 4 , CFastaOstream::fMapMasksUp = 1 << 5 , CFastaOstream::fMapMasksDown = 1 << 6 , CFastaOstream::fNoExpensiveOps = 1 << 7 ,   CFastaOstream::fShowModifiers = 1 << 8 , CFastaOstream::fNoDupCheck = 1 << 9 , CFastaOstream::fShowGapModifiers = 1 << 10 , CFastaOstream::fKeepUnknGapNomLen = 1 << 11 ,   CFastaOstream::fShowGapsOfSizeZero = 1 << 12 , CFastaOstream::fEnableGI = 1 << 13 , CFastaOstream::fHideGenBankPrefix = 1 << 14 , CFastaOstream::fHTMLEncode = 1 << 15 ,   CFastaOstream::fIgnoreOriginalID = 1 << 16 , CFastaOstream::eAssembleParts = fAssembleParts , CFastaOstream::eInstantiateGaps = fInstantiateGaps , CFastaOstream::fUseAutoDef = 1 << 17 ,   CFastaOstream::fBaseFirstUnused = 1 << 18 , CFastaOstream::fDoNotUseAutoDef = 1 << 19 , CFastaOstream::fShowGnlAndAcc = 1 << 20 }
enum	CFastaOstream::EGapMode { CFastaOstream::eGM_one_dash , CFastaOstream::eGM_dashes , CFastaOstream::eGM_letters , CFastaOstream::eGM_count }
	How to represent gaps with fInstantiateGaps enabled, as it is by default. More...
enum	CFastaOstream::EMaskType { CFastaOstream::eSoftMask = 1 , CFastaOstream::eHardMask = 2 }
	Which residues to mask out in subsequent output. More...
enum	CCdregion_translate::ETranslationLengthProblemOptions { CCdregion_translate::eThrowException = 0 , CCdregion_translate::eTruncate , CCdregion_translate::ePad }
enum	CSeqTranslator::ETranslationFlags {   CSeqTranslator::fDefault = 0 , CSeqTranslator::fNoStop = (1<<0) , CSeqTranslator::fRemoveTrailingX = (1<<1) , CSeqTranslator::fIs5PrimePartial = (1<<2) ,   CSeqTranslator::fIs3PrimePartial = (1<<3) }
enum	SRelLoc::EFlags { SRelLoc::fNoMerge = 0x1 }
enum	CSeqSearch::ESearchFlag { CSeqSearch::fNoFlags = 0 , CSeqSearch::fJustTopStrand = 1 , CSeqSearch::fExpandPattern = 2 , CSeqSearch::fAllowMismatch = 4 }
enum	CSequenceAmbigTrimmer::EMeaningOfAmbig { CSequenceAmbigTrimmer::eMeaningOfAmbig_OnlyCompletelyUnknown , CSequenceAmbigTrimmer::eMeaningOfAmbig_AnyAmbig }
	This enum is used to set what is meant by "ambiguous". More...
enum	CSequenceAmbigTrimmer::EFlags { CSequenceAmbigTrimmer::fFlags_DoNotTrimBeginning = (1 << 0) , CSequenceAmbigTrimmer::fFlags_DoNotTrimEnd = (1 << 1) , CSequenceAmbigTrimmer::fFlags_DoNotTrimSeqGap = (1 << 2) }
enum	CSequenceAmbigTrimmer::EResult { CSequenceAmbigTrimmer::eResult_SuccessfullyTrimmed , CSequenceAmbigTrimmer::eResult_NoTrimNeeded }
	This indicates what happened with the trim. More...
enum	CBioseqGaps_CI::EFindNext { CBioseqGaps_CI::eFindNext_NotFound , CBioseqGaps_CI::eFindNext_Found }
	This indicates what happened when we tried to run x_FindNextGapOnBioseq. More...

Functions
	CDeflineGenerator::CDeflineGenerator (void)
	Constructor. More...
	CDeflineGenerator::CDeflineGenerator (const CSeq_entry_Handle &tseh)
	Constructor. More...
	CDeflineGenerator::~CDeflineGenerator (void)
	Destructor. More...
string	CDeflineGenerator::GenerateDefline (const CBioseq_Handle &bsh, TUserFlags flags=0)
	Main method. More...
string	CDeflineGenerator::GenerateDefline (const CBioseq_Handle &bsh, CSeqEntryIndex &idx, TUserFlags flags=0)
	Main method. More...
string	CDeflineGenerator::GenerateDefline (const CBioseq &bioseq, CScope &scope, CSeqEntryIndex &idx, TUserFlags flags=0)
	Main method. More...
string	CDeflineGenerator::GenerateDefline (const CBioseq_Handle &bsh, feature::CFeatTree &ftree, TUserFlags flags=0)
	Main method. More...
string	CDeflineGenerator::GenerateDefline (const CBioseq &bioseq, CScope &scope, TUserFlags flags=0)
	Main method. More...
string	CDeflineGenerator::GenerateDefline (const CBioseq &bioseq, CScope &scope, feature::CFeatTree &ftree, TUserFlags flags=0)
	Main method. More...
string	CDeflineGenerator::x_GetModifiers (const CBioseq_Handle &handle)
bool	CDeflineGenerator::UsePDBCompoundForDefline (void) const
	CDeflineGenerator::CDeflineGenerator (const CDeflineGenerator &)
CDeflineGenerator &	CDeflineGenerator::operator= (const CDeflineGenerator &)
void	CDeflineGenerator::x_Init (void)
	internal methods More...
void	CDeflineGenerator::x_SetFlags (const CBioseq_Handle &bsh, TUserFlags flags)
void	CDeflineGenerator::x_SetFlagsIdx (const CBioseq_Handle &bsh, TUserFlags flags)
void	CDeflineGenerator::x_SetBioSrc (const CBioseq_Handle &bsh)
void	CDeflineGenerator::x_SetBioSrcIdx (const CBioseq_Handle &bsh)
const char *	CDeflineGenerator::x_OrganelleName (CBioSource::TGenome genome) const
bool	CDeflineGenerator::x_CDShasLowQualityException (const CSeq_feat &sft)
void	CDeflineGenerator::x_DescribeClones (vector< CTempString > &desc, string &buf)
CConstRef< CSeq_feat >	CDeflineGenerator::x_GetLongestProtein (const CBioseq_Handle &bsh)
CConstRef< CGene_ref >	CDeflineGenerator::x_GetGeneRefViaCDS (const CMappedFeat &mapped_cds)
void	CDeflineGenerator::x_SetTitleFromBioSrc (void)
void	CDeflineGenerator::x_SetTitleFromNC (void)
void	CDeflineGenerator::x_SetTitleFromNM (const CBioseq_Handle &bsh)
void	CDeflineGenerator::x_SetTitleFromNR (const CBioseq_Handle &bsh)
void	CDeflineGenerator::x_SetTitleFromPatent (void)
void	CDeflineGenerator::x_SetTitleFromPDB (void)
void	CDeflineGenerator::x_SetTitleFromGPipe (void)
void	CDeflineGenerator::x_SetTitleFromProtein (const CBioseq_Handle &bsh)
void	CDeflineGenerator::x_SetTitleFromProteinIdx (const CBioseq_Handle &bsh)
void	CDeflineGenerator::x_SetTitleFromSegSeq (const CBioseq_Handle &bsh)
void	CDeflineGenerator::x_SetTitleFromWGS (void)
void	CDeflineGenerator::x_SetTitleFromMap (void)
void	CDeflineGenerator::x_SetPrefix (string &prefix, const CBioseq_Handle &bsh)
void	CDeflineGenerator::x_SetSuffix (string &suffix, const CBioseq_Handle &bsh, bool appendComplete)
void	CDeflineGenerator::x_AdjustProteinTitleSuffix (const CBioseq_Handle &bsh)
void	CDeflineGenerator::x_AdjustProteinTitleSuffixIdx (const CBioseq_Handle &bsh)
bool	CDeflineGenerator::x_IsComplete () const
	CDeflineGenerator::CLowQualityTextFsm::CLowQualityTextFsm (void)
virtual	CGetOverlappingFeaturesPlugin::~CGetOverlappingFeaturesPlugin ()
virtual void	CGetOverlappingFeaturesPlugin::processSAnnotSelector (SAnnotSelector &sel)=0
virtual void	CGetOverlappingFeaturesPlugin::setUpFeatureIterator (CBioseq_Handle &bioseq_handle, unique_ptr< CFeat_CI > &feat_ci, TSeqPos circular_length, CRange< TSeqPos > &range, const CSeq_loc &loc, SAnnotSelector &sel, CScope &scope, ENa_strand &strand)=0
virtual void	CGetOverlappingFeaturesPlugin::processLoc (CBioseq_Handle &bioseq_handle, CRef< CSeq_loc > &loc, TSeqPos circular_length)=0
virtual void	CGetOverlappingFeaturesPlugin::processMainLoop (bool &shouldContinueToNextIteration, CRef< CSeq_loc > &cleaned_loc_this_iteration, CRef< CSeq_loc > &candidate_feat_loc, EOverlapType &overlap_type_this_iteration, bool &revert_locations_this_iteration, CBioseq_Handle &bioseq_handle, const CMappedFeat &feat, TSeqPos circular_length, SAnnotSelector::EOverlapType annot_overlap_type)=0
virtual void	CGetOverlappingFeaturesPlugin::postProcessDiffAmount (Int8 &cur_diff, CRef< CSeq_loc > &cleaned_loc_this_iteration, CRef< CSeq_loc > &candidate_feat_loc, CScope &scope, SAnnotSelector &sel, TSeqPos circular_length)=0
virtual const char *	CSeqIdFromHandleException::GetErrCodeString (void) const override
	CSeqIdFromHandleException::NCBI_EXCEPTION_DEFAULT (CSeqIdFromHandleException, CException)
	CFastaOstream::CFastaOstream (CNcbiOstream &out)
virtual	CFastaOstream::~CFastaOstream ()
virtual void	CFastaOstream::Write (const CSeq_entry_Handle &handle, const CSeq_loc *location=0)
	Unspecified locations designate complete sequences; non-empty custom titles override the usual title determination logic. More...
virtual void	CFastaOstream::Write (const CBioseq_Handle &handle, const CSeq_loc *location=0, const string &custom_title=kEmptyStr)
virtual void	CFastaOstream::WriteTitle (const CBioseq_Handle &handle, const CSeq_loc *location=0, const string &custom_title=kEmptyStr)
virtual void	CFastaOstream::WriteSequence (const CBioseq_Handle &handle, const CSeq_loc *location=0, CSeq_loc::EOpFlags merge_flags=CSeq_loc::fMerge_AbuttingOnly)
void	CFastaOstream::Write (const CSeq_entry &entry, const CSeq_loc *location=0, bool no_scope=false)
	These versions may set up a temporary object manager scope In the common case of a raw bioseq, no scope is needed. More...
void	CFastaOstream::Write (const CBioseq &seq, const CSeq_loc *location=0, bool no_scope=false, const string &custom_title=kEmptyStr)
void	CFastaOstream::WriteTitle (const CBioseq &seq, const CSeq_loc *location=0, bool no_scope=false, const string &custom_title=kEmptyStr)
virtual bool	CFastaOstream::SkipBioseq (const CBioseq &)
	Used only by Write(CSeq_entry[_Handle], ...); permissive by default. More...
virtual bool	CFastaOstream::SkipBioseq (const CBioseq_Handle &handle)
	Delegates to the non-handle version by default for compatibility with older code; newer code should override this version. More...
CConstRef< CSeq_loc >	CFastaOstream::GetMask (EMaskType type) const
void	CFastaOstream::SetMask (EMaskType type, CConstRef< CSeq_loc > location)
TSeqPos	CFastaOstream::GetWidth (void) const
	Other parameters... More...
void	CFastaOstream::SetWidth (TSeqPos width)
TFlags	CFastaOstream::GetAllFlags (void) const
void	CFastaOstream::SetAllFlags (TFlags flags)
void	CFastaOstream::SetFlag (EFlags flag)
void	CFastaOstream::ResetFlag (EFlags flag)
void	CFastaOstream::SetGapMode (EGapMode mode)
EGapMode	CFastaOstream::GetGapMode (void) const
void	CFastaOstream::SGapModText::WriteAllModsAsFasta (CNcbiOstream &out) const
	This will write the modifiers in FASTA format. More...
static void	CFastaOstream::GetGapModText (const CSeq_gap &seq_gap, SGapModText &out_gap_mod_text)
	Given a CSeq_gap object, this outputs the Gap information. More...
virtual void	CFastaOstream::x_WriteSeqIds (const CBioseq &bioseq, const CSeq_loc *location)
virtual void	CFastaOstream::x_WriteAsFasta (const CBioseq &bioseq)
virtual void	CFastaOstream::x_GetBestId (CConstRef< CSeq_id > &gi_id, CConstRef< CSeq_id > &best_id, bool &hide_prefix, const CBioseq &bioseq)
virtual void	CFastaOstream::x_WriteSeqTitle (const CBioseq_Handle &handle, const string &custom_title)
virtual void	CFastaOstream::x_WriteBuffer (const char *buf, unsigned int count)
sequence::CDeflineGenerator::TUserFlags	CFastaOstream::x_GetTitleFlags (void) const
CConstRef< CSeq_loc >	CFastaOstream::x_MapMask (CSeq_loc_Mapper &mapper, const CSeq_loc &mask, const CSeq_id *base_seq_id, CScope *scope)
void	CFastaOstream::x_GetMaskingStates (TMSMap &masking_states, const CSeq_id *base_seq_id, const CSeq_loc *location, CScope *scope)
void	CFastaOstream::x_WriteSequence (const CSeqVector &vec, const TMSMap &masking_state)
static void	CCdregion_translate::TranslateCdregion (string &prot, const CBioseq_Handle &bsh, const CSeq_loc &loc, const CCdregion &cdr, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=0, ETranslationLengthProblemOptions options=eThrowException)
	translation coding region into ncbieaa protein sequence More...
static void	CCdregion_translate::TranslateCdregion (string &prot, const CSeq_feat &cds, CScope &scope, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=0, ETranslationLengthProblemOptions options=eThrowException)
static void	CSeqTranslator::Translate (const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)
	Translate a string using a specified genetic code. More...
static void	CSeqTranslator::Translate (const string &seq, string &prot, TTranslationFlags flags=fDefault, const CGenetic_code *code=NULL, bool *alt_start=NULL)
	Translate a string using a specified genetic code. More...
static void	CSeqTranslator::Translate (const CSeqVector &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)
	Translate a seq-vector using a specified genetic code if the code is NULL, then the default genetic code is used. More...
static void	CSeqTranslator::Translate (const CSeqVector &seq, string &prot, TTranslationFlags flags=fDefault, const CGenetic_code *code=NULL, bool *alt_start=NULL)
	Translate a seq-vector using a specified genetic code if the code is NULL, then the default genetic code is used. More...
static void	CSeqTranslator::Translate (const CSeq_loc &loc, const CBioseq_Handle &handle, string &prot, const CGenetic_code *code=NULL, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=0)
	utility function: translate a given location on a sequence More...
static void	CSeqTranslator::Translate (const CSeq_loc &loc, CScope &scope, string &prot, const CGenetic_code *code=NULL, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=0)
	utility function: translate a given location on a sequence More...
static void	CSeqTranslator::Translate (const CSeq_feat &cds, CScope &scope, string &prot, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=0)
	Translate a CDRegion into a protein. More...
static CRef< CBioseq >	CSeqTranslator::TranslateToProtein (const CSeq_feat &cds, CScope &scope)
static bool	CSeqTranslator::ChangeDeltaProteinToRawProtein (CRef< CBioseq > protein)
static CCdregion::EFrame	CSeqTranslator::FindBestFrame (const CSeq_feat &cds, CScope &scope)
	Find "best" frame for a coding region. More...
static CCdregion::EFrame	CSeqTranslator::FindBestFrame (const CSeq_feat &cds, CScope &scope, bool &ambiguous)
	SRelLoc::SRelLoc (const CSeq_loc &parent, const CSeq_loc &child, CScope *scope=0, TFlags flags=0)
	Beware: treats locations corresponding to different sequences as disjoint, even if one is actually a segment of the other. More...
	SRelLoc::SRelLoc (const CSeq_loc &parent, const TRanges &ranges)
	For manual work. As noted above, ranges need not contain any IDs. More...
CRef< CSeq_loc >	SRelLoc::Resolve (CScope *scope=0, TFlags flags=0) const
CRef< CSeq_loc >	SRelLoc::Resolve (const CSeq_loc &new_parent, CScope *scope=0, TFlags flags=0) const
	CSeqSearch::CPatternInfo::CPatternInfo (const string &name, const string &sequence, Int2 cut_site)
	constructor More...
const string &	CSeqSearch::CPatternInfo::GetName (void) const
const string &	CSeqSearch::CPatternInfo::GetSequence (void) const
Int2	CSeqSearch::CPatternInfo::GetCutSite (void) const
ENa_strand	CSeqSearch::CPatternInfo::GetStrand (void) const
virtual	CSeqSearch::IClient::~IClient ()
virtual bool	CSeqSearch::IClient::OnPatternFound (const TPatternInfo &pat_info, TSeqPos pos)=0
	CSeqSearch::CSeqSearch (IClient *client=0, TSearchFlags flags=fNoFlags)
	constructors More...
	CSeqSearch::~CSeqSearch (void)
	destructor More...
void	CSeqSearch::AddNucleotidePattern (const string &name, const string &sequence, Int2 cut_site, TSearchFlags flags=fNoFlags)
	Add nucleotide pattern or restriction site to sequence search. More...
void	CSeqSearch::Search (const CBioseq_Handle &seq)
	Search the sequence for patterns. More...
int	CSeqSearch::Search (int current_state, char ch, int position, int length=kMax_Int)
	Low level search method. More...
const IClient *	CSeqSearch::GetClient () const
	Get / Set client. More...
void	CSeqSearch::SetClient (IClient *client)
void	CSeqSearch::x_AddNucleotidePattern (const string &name, string &pattern, Int2 cut_site, ENa_strand strand, TSearchFlags flags)
void	CSeqSearch::x_ExpandPattern (string &sequence, string &buffer, size_t pos, TPatternInfo &pat_info, TSearchFlags flags)
void	CSeqSearch::x_AddPattern (TPatternInfo &pat_info, string &sequence, TSearchFlags flags)
void	CSeqSearch::x_StorePattern (TPatternInfo &pat_info, string &sequence)
bool	CSeqSearch::x_IsJustTopStrand (TSearchFlags flags) const
bool	CSeqSearch::x_IsExpandPattern (TSearchFlags flags) const
bool	CSeqSearch::x_IsAllowMismatch (TSearchFlags flags) const
static const TTrimRuleVec &	CSequenceAmbigTrimmer::GetDefaultTrimRules (void)
	This returns a reasonable default for trimming rules. More...
	CSequenceAmbigTrimmer::CSequenceAmbigTrimmer (EMeaningOfAmbig eMeaningOfAmbig, TFlags fFlags=0, const TTrimRuleVec &vecTrimRules=GetDefaultTrimRules(), TSignedSeqPos uMinSeqLen=50)
	This sets up the parameters for how this trimmer will act. More...
virtual	CSequenceAmbigTrimmer::~CSequenceAmbigTrimmer ()
	Do-nothing destructor just to allow inheritance. More...
virtual EResult	CSequenceAmbigTrimmer::DoTrim (CBioseq_Handle &bioseq_handle, CRangeCollection< TSeqPos > *trimmed_ranges=nullptr)
	This trims the given bioseq, using params set in the CSequenceAmbigTrimmer constructor. More...
bool	CSequenceAmbigTrimmer::x_TestFlag (TFlags fFlag)
	Test if a given flag is set. More...
virtual void	CSequenceAmbigTrimmer::x_NormalizeVecTrimRules (TTrimRuleVec &vecTrimRules)
	This prepares the vector of trimming rules to be used by the trimming algorithm. More...
virtual EResult	CSequenceAmbigTrimmer::x_TrimToNothing (CBioseq_Handle &bioseq_handle)
	The bioseq is trimmed to size 0. More...
virtual TSignedSeqPos	CSequenceAmbigTrimmer::x_FindWhereToTrim (const CSeqVector &seqvec, const TSignedSeqPos iStartPosInclusive_arg, const TSignedSeqPos iEndPosInclusive_arg, TSignedSeqPos iTrimDirection)
	This returns the last good base that won't be trimmed (note: last really means "first" when we're starting from the end) More...
virtual void	CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust (const CSeqVector &seqvec, TSignedSeqPos &in_out_uStartOfGoodBasesSoFar, const TSignedSeqPos uEndOfGoodBasesSoFar, const TSignedSeqPos iTrimDirection, const TSignedSeqPos uChunkSize)
	This adjusts in_out_uStartOfGoodBasesSoFar if we're at a CSeqMap gap. More...
	CSequenceAmbigTrimmer::SAmbigCount::SAmbigCount (const TSignedSeqPos iTrimDirection)
virtual void	CSequenceAmbigTrimmer::x_CountAmbigInRange (SAmbigCount &out_result, const CSeqVector &seqvec, const TSignedSeqPos iStartPosInclusive_arg, const TSignedSeqPos iEndPosInclusive_arg, const TSignedSeqPos iTrimDirection)
	This counts the number of ambiguous bases in the range [leftmost_pos_to_check, rightmost_pos_to_check]. More...
TSignedSeqPos	CSequenceAmbigTrimmer::x_SegmentGetBeginningInclusive (const CSeqMap_CI &segment, const TSignedSeqPos iTrimDirection)
	This returns the (inclusive) position at the beginning of the segment. More...
TSignedSeqPos	CSequenceAmbigTrimmer::x_SegmentGetEndInclusive (const CSeqMap_CI &segment, const TSignedSeqPos iTrimDirection)
	This returns the (inclusive) position at the end of the segment currently at iStartPosInclusive_arg. More...
CSeqMap_CI &	CSequenceAmbigTrimmer::x_SeqMapIterDoNext (CSeqMap_CI &in_out_segment_it, const TSignedSeqPos iTrimDirection)
	Returns the "next" segment. More...
void	CSequenceAmbigTrimmer::x_SliceBioseq (TSignedSeqPos leftmost_good_base, TSignedSeqPos rightmost_good_base, CBioseq_Handle &bioseq_handle)
	CBioseqGaps_CI::Params::Params (void)
	Default ctor gives params which are usually reasonable. More...
	CBioseqGaps_CI::CBioseqGaps_CI (const CSeq_entry_Handle &entry_h, const Params &params=Params())
	This constructor initializes the iterator. More...
CBioseqGaps_CI &	CBioseqGaps_CI::operator++ (void)
	Move the iterator forward to next gap (or the end, if there are no more to return) More...
	CBioseqGaps_CI::DECLARE_OPERATOR_BOOL (m_bioseq_CI)
	CBioseqGaps_CI::SCurrentGapInfo::SCurrentGapInfo (void)
	Constructor initializes to state that it should be when the iterator first starts. More...
const SCurrentGapInfo &	CBioseqGaps_CI::operator* (void) const
	Get information about the gap we're currently on. More...
const SCurrentGapInfo *	CBioseqGaps_CI::operator-> (void) const
	Get information about the gap we're currently on. More...
virtual const SCurrentGapInfo &	CBioseqGaps_CI::x_GetCurrent (void) const
	This gives info on the gap we're currently on. More...
virtual void	CBioseqGaps_CI::x_Next (void)
	This moves this iterator to the next relevant gap. More...
virtual void	CBioseqGaps_CI::x_NextBioseq (void)
	This advances m_bioseq_CI although it has extra logic to terminate m_bioseq_CI if we've exceeded the number of bioseqs we can look for. More...
virtual EFindNext	CBioseqGaps_CI::x_FindNextGapOnBioseq (const CBioseq_Handle &bioseq_h, const TSeqPos pos_to_start_looking, TSeqPos &out_pos_of_gap, TSeqPos &out_len_of_gap) const
	This finds the next gap on the bioseq, starting at given pos. More...

Variables
CRef< CSeqEntryIndex >	CDeflineGenerator::m_Idx
	index with feature tree for each Bioseq More...
CSeq_entry_Handle	CDeflineGenerator::m_TopSEH
	internal feature tree for parent mapping More...
CRef< feature::CFeatTree >	CDeflineGenerator::m_Feat_Tree
bool	CDeflineGenerator::m_ConstructedFeatTree
bool	CDeflineGenerator::m_InitializedFeatTree
bool	CDeflineGenerator::m_Reconstruct
	ignore existing title is forced for certain types More...
bool	CDeflineGenerator::m_AllProtNames
bool	CDeflineGenerator::m_LocalAnnotsOnly
bool	CDeflineGenerator::m_GpipeMode
bool	CDeflineGenerator::m_OmitTaxonomicName
bool	CDeflineGenerator::m_DevMode
bool	CDeflineGenerator::m_IsNA
	seq-inst fields More...
bool	CDeflineGenerator::m_IsAA
CSeq_inst::TTopology	CDeflineGenerator::m_Topology
CSeq_inst::TLength	CDeflineGenerator::m_Length
bool	CDeflineGenerator::m_IsSeg
bool	CDeflineGenerator::m_IsDelta
bool	CDeflineGenerator::m_IsVirtual
bool	CDeflineGenerator::m_IsMap
bool	CDeflineGenerator::m_IsNC
	seq-id fields More...
bool	CDeflineGenerator::m_IsNM
bool	CDeflineGenerator::m_IsNR
bool	CDeflineGenerator::m_IsNZ
bool	CDeflineGenerator::m_IsPatent
bool	CDeflineGenerator::m_IsPDB
bool	CDeflineGenerator::m_IsWP
bool	CDeflineGenerator::m_ThirdParty
bool	CDeflineGenerator::m_WGSMaster
bool	CDeflineGenerator::m_TSAMaster
bool	CDeflineGenerator::m_TLSMaster
string	CDeflineGenerator::m_MainTitle
string	CDeflineGenerator::m_GeneralStr
int	CDeflineGenerator::m_GeneralId
string	CDeflineGenerator::m_PatentCountry
string	CDeflineGenerator::m_PatentNumber
int	CDeflineGenerator::m_PatentSequence
int	CDeflineGenerator::m_PDBChain
string	CDeflineGenerator::m_PDBChainID
CMolInfo::TBiomol	CDeflineGenerator::m_MIBiomol
	molinfo fields More...
CMolInfo::TTech	CDeflineGenerator::m_MITech
CMolInfo::TCompleteness	CDeflineGenerator::m_MICompleteness
bool	CDeflineGenerator::m_HTGTech
bool	CDeflineGenerator::m_HTGSUnfinished
bool	CDeflineGenerator::m_IsTLS
bool	CDeflineGenerator::m_IsTSA
bool	CDeflineGenerator::m_IsWGS
bool	CDeflineGenerator::m_IsEST_STS_GSS
bool	CDeflineGenerator::m_UseBiosrc
bool	CDeflineGenerator::m_HTGSCancelled
	genbank or embl block keyword fields More...
bool	CDeflineGenerator::m_HTGSDraft
bool	CDeflineGenerator::m_HTGSPooled
bool	CDeflineGenerator::m_TPAExp
bool	CDeflineGenerator::m_TPAInf
bool	CDeflineGenerator::m_TPAReasm
bool	CDeflineGenerator::m_Unordered
CTempString	CDeflineGenerator::m_PDBCompound
	pdb block fields More...
CConstRef< CBioSource >	CDeflineGenerator::m_Source
	biosource fields More...
CTempString	CDeflineGenerator::m_Taxname
CTempString	CDeflineGenerator::m_Genus
CTempString	CDeflineGenerator::m_Species
bool	CDeflineGenerator::m_Multispecies
CBioSource::TGenome	CDeflineGenerator::m_Genome
bool	CDeflineGenerator::m_IsPlasmid
bool	CDeflineGenerator::m_IsChromosome
CTempString	CDeflineGenerator::m_Organelle
string	CDeflineGenerator::m_FirstSuperKingdom
string	CDeflineGenerator::m_SecondSuperKingdom
bool	CDeflineGenerator::m_IsCrossKingdom
CTempString	CDeflineGenerator::m_Chromosome
	subsource fields More...
CTempString	CDeflineGenerator::m_LinkageGroup
CTempString	CDeflineGenerator::m_Clone
bool	CDeflineGenerator::m_has_clone
CTempString	CDeflineGenerator::m_Map
CTempString	CDeflineGenerator::m_Plasmid
CTempString	CDeflineGenerator::m_Segment
CTempString	CDeflineGenerator::m_Breed
	orgmod fields More...
CTempString	CDeflineGenerator::m_Cultivar
CTempString	CDeflineGenerator::m_SpecimenVoucher
CTempString	CDeflineGenerator::m_Isolate
CTempString	CDeflineGenerator::m_Strain
CTempString	CDeflineGenerator::m_Substrain
CTempString	CDeflineGenerator::m_MetaGenomeSource
bool	CDeflineGenerator::m_IsUnverified
	user object fields More...
CTempString	CDeflineGenerator::m_UnverifiedPrefix
bool	CDeflineGenerator::m_IsUnreviewed
CTempString	CDeflineGenerator::m_UnreviewedPrefix
CTempString	CDeflineGenerator::m_TargetedLocus
CTempString	CDeflineGenerator::m_Comment
	comment fields More...
bool	CDeflineGenerator::m_IsPseudogene
string	CDeflineGenerator::m_rEnzyme
	map fields More...
bool	CDeflineGenerator::m_UsePDBCompoundForDefline
bool	CDeflineGenerator::m_FastaFormat
static CSafeStatic< CLowQualityTextFsm >	CDeflineGenerator::ms_p_Low_Quality_Fsa
string	CFastaOstream::SGapModText::gap_type
	String representing the gap type. More...
vector< string >	CFastaOstream::SGapModText::gap_linkage_evidences
	A vector representing the linkage-evidences of the gap. More...
CNcbiOstream &	CFastaOstream::m_Out
unique_ptr< sequence::CDeflineGenerator >	CFastaOstream::m_Gen
TFlags	CFastaOstream::m_Flags
CConstRef< CSeq_loc >	CFastaOstream::m_SoftMask
CConstRef< CSeq_loc >	CFastaOstream::m_HardMask
TSeqPos	CFastaOstream::m_Width
EGapMode	CFastaOstream::m_GapMode
TSeq_id_HandleSet	CFastaOstream::m_PreviousWholeIds
TCharBuf	CFastaOstream::m_Dashes
TCharBuf	CFastaOstream::m_LC_Ns
TCharBuf	CFastaOstream::m_LC_Xs
TCharBuf	CFastaOstream::m_UC_Ns
TCharBuf	CFastaOstream::m_UC_Xs
CConstRef< CSeq_loc >	SRelLoc::m_ParentLoc
TRanges	SRelLoc::m_Ranges
string	CSeqSearch::CPatternInfo::m_Name
	data More...
string	CSeqSearch::CPatternInfo::m_Sequence
	user defined name More...
Int2	CSeqSearch::CPatternInfo::m_CutSite
	nucleotide sequence More...
ENa_strand	CSeqSearch::CPatternInfo::m_Strand
IClient *	CSeqSearch::m_Client
TSearchFlags	CSeqSearch::m_Flags
size_t	CSeqSearch::m_LongestPattern
CTextFsm< TPatternInfo >	CSeqSearch::m_Fsa
TSignedSeqPos	CSequenceAmbigTrimmer::STrimRule::bases_to_check
TSignedSeqPos	CSequenceAmbigTrimmer::STrimRule::max_bases_allowed_to_be_ambig
EMeaningOfAmbig	CSequenceAmbigTrimmer::m_eMeaningOfAmbig
	This holds the current interpretation for "ambiguous". More...
TFlags	CSequenceAmbigTrimmer::m_fFlags
	This holds the flags that affect the behavior of this class. More...
TTrimRuleVec	CSequenceAmbigTrimmer::m_vecTrimRules
	This holds the trimming rules that will be applied. More...
TSignedSeqPos	CSequenceAmbigTrimmer::m_uMinSeqLen
	When the bioseq gets trimmed down to less than this size, we halt the trimming. More...
TSignedSeqPos	CSequenceAmbigTrimmer::SAmbigCount::num_ambig_bases
	the number of ambiguous bases found in the range supplied to x_CountAmbigInRange More...
TSignedSeqPos	CSequenceAmbigTrimmer::SAmbigCount::pos_after_last_gap
	Inclusive. More...
TAmbigLookupTable	CSequenceAmbigTrimmer::m_arrNucAmbigLookupTable
TAmbigLookupTable	CSequenceAmbigTrimmer::m_arrProtAmbigLookupTable
TSeqPos	CBioseqGaps_CI::Params::max_gap_len_to_ignore
	We completely ignore any gaps we find that have this number of bases or fewer. More...
TSeqPos	CBioseqGaps_CI::Params::max_num_gaps_per_seq
	We only return up to this many gaps for each sequence. More...
TSeqPos	CBioseqGaps_CI::Params::max_num_seqs
	We only return gaps on up to this many sequences. More...
CSeq_inst::EMol	CBioseqGaps_CI::Params::mol_filter
	CSeq_inst::eMol_na to only look at gaps on nucleotide sequences. More...
CBioseq_CI::EBioseqLevelFlag	CBioseqGaps_CI::Params::level_filter
	Works like the level filter in CBioseq_CI. More...
CSeq_id_Handle	CBioseqGaps_CI::SCurrentGapInfo::seq_id
	The seq-id that this gap is on. More...
size_t	CBioseqGaps_CI::SCurrentGapInfo::num_seqs_seen_so_far
	This indicates how many sequences we've seen so far, including the one we're currently on. More...
TSeqPos	CBioseqGaps_CI::SCurrentGapInfo::start_pos
	the 0-based position at which the current gap starts on the current sequence. More...
TSeqPos	CBioseqGaps_CI::SCurrentGapInfo::length
	the length of the current gap More...
size_t	CBioseqGaps_CI::SCurrentGapInfo::num_gaps_seen_so_far_on_this_seq
	how many gaps we've seen so far on this sequence. More...
CBioseq_CI	CBioseqGaps_CI::m_bioseq_CI
	This points to the bioseq we're currently on. More...
SCurrentGapInfo	CBioseqGaps_CI::m_infoOnCurrentGap
	This indicates information about the gap we're currently on. More...
Params	CBioseqGaps_CI::m_Params
	This holds the params the caller gave when this object was initially created. More...

Friends
class	CSeqSearch::CPatternInfo::CSeqSearch

SeqIdConv
Conversions between seq-id types
enum	EAccessionVersion { eWithAccessionVersion , eWithoutAccessionVersion }
enum	EGetIdFlags {   eGetId_ForceGi = 0x0000 , eGetId_ForceAcc = 0x0001 , eGetId_Best = 0x0002 , eGetId_HandleDefault = 0x0003 ,   eGetId_Seq_id_Score = 0x0004 , eGetId_Seq_id_BestRank = 0x0005 , eGetId_Seq_id_WorstRank = 0x0006 , eGetId_Seq_id_FastaAARank = 0x0007 ,   eGetId_Seq_id_FastaNARank = 0x0008 , eGetId_Canonical = eGetId_Seq_id_BestRank , eGetId_TypeMask = 0x00FF , eGetId_VerifyId = 0x0100 ,   eGetId_ThrowOnError = 0x0200 , eGetId_Default = eGetId_Best | eGetId_ThrowOnError }
	Retrieve a particular seq-id from a given bioseq handle. More...
typedef int	EGetIdType
TGi	GetGiForAccession (const string &acc, CScope &scope, EGetIdType flags=0)
	Given an accession string retrieve the GI id. More...
string	GetAccessionForGi (TGi gi, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0)
	Retrieve the accession for a given GI. More...
TGi	GetGiForId (const objects::CSeq_id &id, CScope &scope, EGetIdType flags=0)
	Given a Seq-id retrieve the corresponding GI. More...
string	GetAccessionForId (const objects::CSeq_id &id, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0)
	Retrieve the accession string for a Seq-id. More...
CSeq_id_Handle	GetId (const CBioseq_Handle &handle, EGetIdType type=eGetId_Default)
	Return a selected ID type for a given bioseq handle. More...
CSeq_id_Handle	GetId (const CSeq_id &id, CScope &scope, EGetIdType type=eGetId_Default)
	Return a selected ID type for a seq-id. More...
CSeq_id_Handle	GetId (const CSeq_id_Handle &id, CScope &scope, EGetIdType type=eGetId_Default)
	Return a selected ID type for a seq-id handle. More...
CSeq_id_Handle	GetId (const CBioseq::TId &id, EGetIdType type=eGetId_Default)
	Return a selected ID type from a set of Seq-ids Arguments (except 'id') and behavior is the same as of GetId(const CSeq_id& id, ...). More...
CSeq_id_Handle	GetId (const CBioseq &seq, EGetIdType type=eGetId_Default)
	Return a selected ID type from a Bioseq Arguments (except 'seq') and behavior is the same as of GetId(const CBioseq_Handle& seq, ...). More...

FindLatestSequence
Walk the replace history to find the latest revision of a sequence
CConstRef< CSeq_id >	FindLatestSequence (const CSeq_id &id, CScope &scope)
	Given a seq-id check its replace history and try to find the latest revision. More...
CSeq_id_Handle	FindLatestSequence (const CSeq_id_Handle &idh, CScope &scope)
CConstRef< CSeq_id >	FindLatestSequence (const CSeq_id &id, CScope &scope, const CTime &tlim)
	Check replace history up to the specified date. More...
CSeq_id_Handle	FindLatestSequence (const CSeq_id_Handle &idh, CScope &scope, const CTime &tlim)

GetTitle
Get sequence's title (used in various flat-file formats.) Deprecated in favor of CDeflineGenerator.
enum	EGetTitleFlags { fGetTitle_Reconstruct = 0x1 , fGetTitle_Organism = 0x2 , fGetTitle_AllProteins = 0x4 , fGetTitle_NoExpensive = 0x8 }
	This function is here rather than in CBioseq because it may need to inspect other sequences. More...
typedef int	TGetTitleFlags
NCBI_XOBJUTIL_EXPORT string	GetTitle (const CBioseq_Handle &hnd, TGetTitleFlags flags=0)
NCBI_XOBJUTIL_EXPORT bool	GetTitle (const CBioseq &seq, string *title_ptr, TGetTitleFlags flags=0)

Source and Product
Mapping locations through features
enum	ES2PFlags { fS2P_NoMerge = 0x1 , fS2P_AllowTer = 0x2 }
enum	EP2SFlags { fP2S_Extend = 0x1 }
typedef int	TS2PFlags
typedef int	TP2SFlags
CRef< CSeq_loc >	SourceToProduct (const CSeq_feat &feat, const CSeq_loc &source_loc, TS2PFlags flags=0, CScope *scope=0, int *frame=0)
CRef< CSeq_loc >	ProductToSource (const CSeq_feat &feat, const CSeq_loc &prod_loc, TP2SFlags flags=0, CScope *scope=0)

Overlapping
Searching for features
enum	EBestFeatOpts {   fBestFeat_StrictMatch = 0x01 , fBestFeat_NoExpensive = 0x02 , fBestFeat_FavorLonger = 0x04 , fBestFeat_IgnoreStrand = 0x08 ,   fBestFeat_Defaults = 0 }
enum	ETransSplicing { eTransSplicing_No = 0 , eTransSplicing_Yes , eTransSplicing_Auto }
	Convenience functions for popular overlapping types. More...
typedef int	TBestFeatOpts
typedef pair< Int8, CConstRef< CSeq_feat > >	TFeatScore
	Storage for features and scores. More...
typedef vector< TFeatScore >	TFeatScores
void	GetOverlappingFeatures (const CSeq_loc &loc, CSeqFeatData::E_Choice feat_type, CSeqFeatData::ESubtype feat_subtype, EOverlapType overlap_type, TFeatScores &feats, CScope &scope, const TBestFeatOpts opts=0, CGetOverlappingFeaturesPlugin *plugin=NULL)
	Find all features overlapping the location. More...
CConstRef< CSeq_feat >	GetBestOverlappingFeat (const CSeq_loc &loc, CSeqFeatData::E_Choice feat_type, EOverlapType overlap_type, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
	See the note above on 'overlap_type' meaning. More...
CConstRef< CSeq_feat >	GetBestOverlappingFeat (const CSeq_loc &loc, CSeqFeatData::ESubtype feat_type, EOverlapType overlap_type, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
	See the note above on 'overlap_type' meaning. More...
CConstRef< CSeq_feat >	GetBestGeneForMrna (const CSeq_feat &mrna_feat, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
CConstRef< CSeq_feat >	GetBestGeneForCds (const CSeq_feat &cds_feat, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
CConstRef< CSeq_feat >	GetBestMrnaForCds (const CSeq_feat &cds_feat, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
CConstRef< CSeq_feat >	GetBestCdsForMrna (const CSeq_feat &mrna_feat, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
void	GetMrnasForGene (const CSeq_feat &gene_feat, CScope &scope, list< CConstRef< CSeq_feat > > &mrna_feats, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
void	GetCdssForGene (const CSeq_feat &gene_feat, CScope &scope, list< CConstRef< CSeq_feat > > &cds_feats, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
CConstRef< CSeq_feat >	GetBestGeneForMrna (const CSeq_feat &mrna_feat, const CTSE_Handle &tse, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
CConstRef< CSeq_feat >	GetBestGeneForCds (const CSeq_feat &cds_feat, const CTSE_Handle &tse, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
CConstRef< CSeq_feat >	GetBestMrnaForCds (const CSeq_feat &cds_feat, const CTSE_Handle &tse, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
CConstRef< CSeq_feat >	GetBestCdsForMrna (const CSeq_feat &mrna_feat, const CTSE_Handle &tse, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
void	GetMrnasForGene (const CSeq_feat &gene_feat, const CTSE_Handle &tse, list< CConstRef< CSeq_feat > > &mrna_feats, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
void	GetCdssForGene (const CSeq_feat &gene_feat, const CTSE_Handle &tse, list< CConstRef< CSeq_feat > > &cds_feats, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
CConstRef< CSeq_feat >	GetBestOverlappingFeat (const CSeq_feat &feat, CSeqFeatData::E_Choice feat_type, sequence::EOverlapType overlap_type, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
CConstRef< CSeq_feat >	GetBestOverlappingFeat (const CSeq_feat &feat, CSeqFeatData::ESubtype feat_type, sequence::EOverlapType overlap_type, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)
CConstRef< CSeq_feat >	GetmRNAforCDS (const CSeq_feat &cds, CScope &scope)
	GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS. More...
CConstRef< CSeq_feat >	GetBestOverlapForSNP (const CSeq_feat &snp_feat, CSeqFeatData::E_Choice type, CScope &scope, bool search_both_strands=true)
	Get the best overlapping feature for a SNP (variation) feature. More...
CConstRef< CSeq_feat >	GetBestOverlapForSNP (const CSeq_feat &snp_feat, CSeqFeatData::ESubtype subtype, CScope &scope, bool search_both_strands=true)
	Get the best overlapping feature for a SNP (variation) More...
CConstRef< CSeq_feat >	GetOverlappingGene (const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)
CConstRef< CSeq_feat >	GetGeneForFeature (const CSeq_feat &feat, CScope &scope)
	Finds gene for feature, but obeys SeqFeatXref directives. More...
bool	IsPseudo (const CSeq_feat &feat, CScope &scope)
	Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to see if a feature is pseudo. More...
CConstRef< CSeq_feat >	GetOverlappingmRNA (const CSeq_loc &loc, CScope &scope)
CConstRef< CSeq_feat >	GetOverlappingCDS (const CSeq_loc &loc, CScope &scope)
CConstRef< CSeq_feat >	GetOverlappingPub (const CSeq_loc &loc, CScope &scope)
CConstRef< CSeq_feat >	GetOverlappingSource (const CSeq_loc &loc, CScope &scope)
CConstRef< CSeq_feat >	GetOverlappingOperon (const CSeq_loc &loc, CScope &scope)
const CSeq_feat *	GetCDSForProduct (const CBioseq &product, CScope *scope)
	Get the encoding CDS feature of a given protein sequence. More...
const CSeq_feat *	GetCDSForProduct (const CBioseq_Handle &product)
CMappedFeat	GetMappedCDSForProduct (const CBioseq_Handle &product)
const CSeq_feat *	GetPROTForProduct (const CBioseq &product, CScope *scope)
	Get the mature peptide feature of a protein. More...
const CSeq_feat *	GetPROTForProduct (const CBioseq_Handle &product)
const CSeq_feat *	GetmRNAForProduct (const CBioseq &product, CScope *scope)
	Get the encoding mRNA feature of a given mRNA (cDNA) bioseq. More...
const CSeq_feat *	GetmRNAForProduct (const CBioseq_Handle &product)
CMappedFeat	GetMappedmRNAForProduct (const CBioseq_Handle &product)

Sequences
Searching for bioseqs etc.
const CBioseq *	GetNucleotideParent (const CBioseq &product, CScope *scope)
	Get the encoding nucleotide sequnce of a protein. More...
CBioseq_Handle	GetNucleotideParent (const CBioseq_Handle &product)
CBioseq_Handle	GetParentForPart (const CBioseq_Handle &part)
	Get the parent bioseq for a part of a segmented bioseq. More...
const COrg_ref &	GetOrg_ref (const CBioseq_Handle &handle)
	Return the org-ref associated with a given sequence. More...
const COrg_ref *	GetOrg_refOrNull (const CBioseq_Handle &handle)
	Return the pointer to org-ref associated with a given sequence or null if there is no org-ref associated with the sequence. More...
TTaxId	GetTaxId (const CBioseq_Handle &handle)
	return the tax-id associated with a given sequence. More...
const CMolInfo *	GetMolInfo (const CBioseq &bioseq)
	Retrieve the MolInfo object for a given bioseq handle. More...
const CMolInfo *	GetMolInfo (const CBioseq_Handle &handle)
const CBioSource *	GetBioSource (const CBioseq &bioseq)
	Retrieve the BioSource object for a given bioseq handle. More...
const CBioSource *	GetBioSource (const CBioseq_Handle &handle)
CBioseq_Handle	GetBioseqFromSeqLoc (const CSeq_loc &loc, CScope &scope, CScope::EGetBioseqFlag flag=CScope::eGetBioseq_Loaded)
	Retrieve the Bioseq Handle from a location. More...
string	GetProteinName (const CBioseq_Handle &seq)
	Return protein name from corresponding Prot-ref feature. More...
CConstRef< CSeq_feat >	GetSourceFeatForProduct (const CBioseq_Handle &bsh)
TTaxId	GetTaxIdForProduct (const CBioseq_Handle &bsh)
void	GetOrg_refForProduct (const CBioseq_Handle &bsh, const COrg_ref *)
const COrg_ref *	GetOrg_refForBioseq (const CBioseq_Handle &bsh)
	Find an Org-ref for the given Bioseq: If it's a protein then look on the source feature of the product. More...
const CBioSource *	GetBioSourceForBioseq (const CBioseq_Handle &bsh)
	Find a BioSource for the given Bioseq: If it's a protein then look for the source feature of the product. More...
void	ReverseComplement (CSeq_inst &seq, CScope *scope)
	Reverse complement a Bioseq in place. More...

Detailed Description

Typedef Documentation

EGetIdType

typedef int EGetIdType

Definition at line 126 of file sequence.hpp.

TAmbigLookupTable

typedef bool CSequenceAmbigTrimmer::TAmbigLookupTable[26]

protected

Definition at line 1566 of file sequence.hpp.

TBestFeatOpts

typedef int TBestFeatOpts

Definition at line 348 of file sequence.hpp.

TCharBuf

typedef AutoPtr<char, ArrayDeleter<char> > CFastaOstream::TCharBuf

private

Definition at line 915 of file sequence.hpp.

TFeatScore

typedef pair<Int8, CConstRef<CSeq_feat> > TFeatScore

Storage for features and scores.

Definition at line 352 of file sequence.hpp.

TFeatScores

typedef vector<TFeatScore> TFeatScores

Definition at line 353 of file sequence.hpp.

TFlags [1/3]

typedef long CFastaOstream::TFlags

binary OR of EFlags

Definition at line 798 of file sequence.hpp.

TFlags [2/3]

typedef int SRelLoc::TFlags

binary OR of EFlags

Definition at line 1128 of file sequence.hpp.

TFlags [3/3]

typedef int CSequenceAmbigTrimmer::TFlags

Definition at line 1309 of file sequence.hpp.

TGetTitleFlags

typedef int TGetTitleFlags

Definition at line 287 of file sequence.hpp.

TMSMap

typedef map<TSeqPos, int> CFastaOstream::TMSMap

private

Definition at line 928 of file sequence.hpp.

TP2SFlags

typedef int TP2SFlags

Definition at line 316 of file sequence.hpp.

TPatternInfo [1/2]

typedef CPatternInfo CSeqSearch::TPatternInfo

Definition at line 1195 of file sequence.hpp.

TPatternInfo [2/2]

typedef CSeqSearch::TPatternInfo CSeqSearch::IClient::TPatternInfo

Definition at line 1207 of file sequence.hpp.

TRange

typedef CSeq_interval SRelLoc::TRange

For relative ranges (ONLY), id is irrelevant and normally unset.

Definition at line 1131 of file sequence.hpp.

TRanges

typedef vector<CRef<TRange> > SRelLoc::TRanges

Definition at line 1132 of file sequence.hpp.

TS2PFlags

typedef int TS2PFlags

Definition at line 306 of file sequence.hpp.

TSearchFlags

typedef unsigned int CSeqSearch::TSearchFlags

binary OR of ESearchFlag

Definition at line 1220 of file sequence.hpp.

TTranslationFlags

typedef int CSeqTranslator::TTranslationFlags

Definition at line 988 of file sequence.hpp.

TTrimRuleVec

typedef vector<STrimRule> CSequenceAmbigTrimmer::TTrimRuleVec

Multiple STrimRules are allowed, which are applied from smallest bases_to_check to largest bases_to_check, and redundant rules are automatically removed.

When a rule is applied, we start over at the first sorted rule again.

Definition at line 1322 of file sequence.hpp.

TUserFlags

typedef int CDeflineGenerator::TUserFlags

Binary "OR" of EUserFlags.

Definition at line 97 of file create_defline.hpp.

Enumeration Type Documentation

EAccessionVersion

enum EAccessionVersion

Enumerator
eWithAccessionVersion	accession.version (when possible)
eWithoutAccessionVersion	accession only, even if version is available

Definition at line 90 of file sequence.hpp.

EBestFeatOpts

enum EBestFeatOpts

Enumerator
fBestFeat_StrictMatch	requires explicit association, rather than analysis based on overlaps
fBestFeat_NoExpensive	don't perform any expensive tests, such as ones that require fetching additional sequences
fBestFeat_FavorLonger	favor longer features over shorter features
fBestFeat_IgnoreStrand	Pay no attention to strands when finding the best feat. This may be useful for, e.g., trans-spliced genes.
fBestFeat_Defaults	default options: do everything

Definition at line 330 of file sequence.hpp.

EErrCode

enum CSeqIdFromHandleException::EErrCode

Enumerator
eNoSynonyms
eRequestedIdNotFound

Definition at line 752 of file sequence.hpp.

EFindNext

enum CBioseqGaps_CI::EFindNext

protected

This indicates what happened when we tried to run x_FindNextGapOnBioseq.

Enumerator
eFindNext_NotFound	No more relevant gaps were found on this bioseq. The other output parameters will be in an undefined state.
eFindNext_Found	Another relevant gap was found, and the output parameters are filled in to represent information about it.

Definition at line 1689 of file sequence.hpp.

EFlags [1/3]

enum CFastaOstream::EFlags : long

Enumerator
fAssembleParts	assemble FAR delta sequences; on by dflt
fInstantiateGaps	honor specifed gap mode; on by default
fSuppressRange	never include location details in defline
fReverseStrand	flip the (implicit) location
fKeepGTSigns	don't convert '>' to '_' in title
fMapMasksUp	honor masks specified at a lower level
fMapMasksDown	honor masks specified at a higher level
fNoExpensiveOps	don't try too hard to find titles
fShowModifiers	show key-value pair modifiers (e.g. "[organism=Homo sapiens]")
fNoDupCheck	skip check for duplicate sequence IDs
fShowGapModifiers	show gap key-value pair modifiers (e.g. "[linkage-evidence=map;strobe]"). Only works if gap mode is eGM_count.
fKeepUnknGapNomLen	Keep unknown gap's nominal length. That is, when a gap has an unknown length but nominal length, use that instead of just making it 100.
fShowGapsOfSizeZero	Use this to show gaps of size zero as a lone hyphen at the end of a line.
fEnableGI	Use this flag to enable GI output in the defline.
fHideGenBankPrefix	Hide gb| prefix for genbank only seq_id's.
fHTMLEncode	Encode the title string for HTML display.
fIgnoreOriginalID	Disregard original ID when constructing defline.
eAssembleParts
eInstantiateGaps
fUseAutoDef	Disregard original ID when constructing defline.
fBaseFirstUnused	first avalailabe for derived classes
fDoNotUseAutoDef
fShowGnlAndAcc	Show general id and accession in the defline.

Definition at line 772 of file sequence.hpp.

EFlags [2/3]

enum SRelLoc::EFlags

Enumerator
fNoMerge	don't merge adjacent intervals

Definition at line 1125 of file sequence.hpp.

EFlags [3/3]

enum CSequenceAmbigTrimmer::EFlags

Enumerator
fFlags_DoNotTrimBeginning	0x01 ("Beginning" as defined by CSeqVector)
fFlags_DoNotTrimEnd	0x02 ("End" as defined by CSeqVector)
fFlags_DoNotTrimSeqGap	0x04 (Seq-gaps are not considered trimmable if this flag is set, only letter gaps (e.g. N's for nucs))

Definition at line 1300 of file sequence.hpp.

EGapMode

enum CFastaOstream::EGapMode

How to represent gaps with fInstantiateGaps enabled, as it is by default.

(Disabling fInstantiateGaps is equivalent to requesting eGM_one_dash.)

Enumerator
eGM_one_dash	A single dash, followed by a line break.
eGM_dashes	Multiple inline dashes.
eGM_letters	Multiple inline Ns or Xs as appropriate (default).
eGM_count	>?N or >?unk100, as appropriate.

Definition at line 803 of file sequence.hpp.

EGetIdFlags

enum EGetIdFlags

Retrieve a particular seq-id from a given bioseq handle.

This uses CSynonymsSet internally to decide which seq-id should be used.

Enumerator
eGetId_ForceGi	return only a gi-based seq-id
eGetId_ForceAcc	return only an accession based seq-id
eGetId_Best	return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function
eGetId_HandleDefault	returns the ID associated with a bioseq-handle
eGetId_Seq_id_Score	use CSeq_id::Score() as the scoring function
eGetId_Seq_id_BestRank	use CSeq_id::BestRank() as the scoring function
eGetId_Seq_id_WorstRank	use CSeq_id::WorstRank() as the scoring function
eGetId_Seq_id_FastaAARank	use CSeq_id::FastaAARank() as the scoring function
eGetId_Seq_id_FastaNARank	use CSeq_id::FastaNARank() as the scoring function "canonical" here means "most specific"; this differs from "best" in that "best" is intended for display purposes
eGetId_Canonical
eGetId_TypeMask	Mask for requested id type.
eGetId_VerifyId	Check if the seq-id is present in the scope.
eGetId_ThrowOnError	Throw exception on errors. If not set, an empty value is returned.
eGetId_Default

Definition at line 98 of file sequence.hpp.

EGetTitleFlags

enum EGetTitleFlags

This function is here rather than in CBioseq because it may need to inspect other sequences.

The reconstruct flag indicates that it should ignore any existing title Seqdesc.

Enumerator
fGetTitle_Reconstruct	ignore existing title Seqdesc.
fGetTitle_Organism	append [organism]
fGetTitle_AllProteins	normally just names the first
fGetTitle_NoExpensive	skip potential expensive operations

Definition at line 281 of file sequence.hpp.

EMaskType

enum CFastaOstream::EMaskType

Which residues to mask out in subsequent output.

These do NOT automatically reset between calls to Write; you must do so yourself by setting them to null.

Enumerator
eSoftMask	write as lowercase rather than uppercase
eHardMask	write as N for nucleotides, X for peptides

Definition at line 847 of file sequence.hpp.

EMeaningOfAmbig

enum CSequenceAmbigTrimmer::EMeaningOfAmbig

This enum is used to set what is meant by "ambiguous".

Enumerator
eMeaningOfAmbig_OnlyCompletelyUnknown	Here, only N for nucleotides and X for amino acids is considered ambiguous.
eMeaningOfAmbig_AnyAmbig	Here, anything that's not certain is considered ambiguous. That is, anything but A, C, G, T for nucleotides, and most amino acids except, for example, B (which can be aspartic acid or asparagine), X (completely ambiguous), etc.

Definition at line 1289 of file sequence.hpp.

EP2SFlags

enum EP2SFlags

Enumerator
fP2S_Extend	if hitting ends, extend to include partial codons

Definition at line 313 of file sequence.hpp.

EResult

enum CSequenceAmbigTrimmer::EResult

This indicates what happened with the trim.

Error states are indicated by an exception, not EResult.

Enumerator
eResult_SuccessfullyTrimmed	Bioseq is now trimmed.
eResult_NoTrimNeeded	Bioseq is left unchanged because it did not need to be trimmed at all. This is NOT an error.

Definition at line 1352 of file sequence.hpp.

ES2PFlags

enum ES2PFlags

Enumerator
fS2P_NoMerge	don't merge adjacent intervals on the product
fS2P_AllowTer	map the termination codon as a legal location

Definition at line 302 of file sequence.hpp.

ESearchFlag

enum CSeqSearch::ESearchFlag

Enumerator
fNoFlags
fJustTopStrand
fExpandPattern
fAllowMismatch

Definition at line 1214 of file sequence.hpp.

ETranslationFlags

enum CSeqTranslator::ETranslationFlags

See also

TTranslationFlags

Enumerator
fDefault
fNoStop	= 0x1 Do not include stop in translation
fRemoveTrailingX	= 0x2 Remove trailing Xs from protein
fIs5PrimePartial	= 0x4 Translate first codon even if not start codon (because sequence is 5' partial)
fIs3PrimePartial	= 0x8 May not end in stop codon (because sequence is 3' partial)

Definition at line 980 of file sequence.hpp.

ETranslationLengthProblemOptions

enum CCdregion_translate::ETranslationLengthProblemOptions

Enumerator
eThrowException
eTruncate
ePad

Definition at line 948 of file sequence.hpp.

ETransSplicing

enum ETransSplicing

Convenience functions for popular overlapping types.

Enumerator
eTransSplicing_No
eTransSplicing_Yes
eTransSplicing_Auto	Ignore overlap strand if the source location has mixed/both strand.

Definition at line 579 of file sequence.hpp.

EUserFlags

enum CDeflineGenerator::EUserFlags

User-settable flags for tuning behavior.

Enumerator
fIgnoreExisting	Generate fresh titles unconditionally.
fAllProteinNames	List all relevant proteins, not just one.
fLocalAnnotsOnly	Never use related sequences' annotations.
fNoExpensiveOps	Refrain from anything that could add substantial overhead.
fGpipeMode	Use GPipe defaults.
fOmitTaxonomicName	Do not add organism suffix to proteins.
fDevMode	Development mode for testing new features.
fShowModifiers	Show key-value pair modifiers (e.g. "[organism=Homo sapiens]")
fUseAutoDef	Run auto-def for nucleotides if user object is present.
fFastaFormat	Generate FASTA defline.
fDoNotUseAutoDef	Disable internal call to auto-def.

Definition at line 83 of file create_defline.hpp.

Function Documentation

AddNucleotidePattern()

void CSeqSearch::AddNucleotidePattern	(	const string &	name,
		const string &	sequence,
		Int2	cut_site,
		TSearchFlags	flags = fNoFlags
	)

Add nucleotide pattern or restriction site to sequence search.

Uses ambiguity codes, e.g., R = A and G, H = A, C and T

Parameters

sequence	pattern's name
cut_site	pattern's sequence

Definition at line 4871 of file sequence.cpp.

References eNa_strand_both, eNa_strand_minus, eNa_strand_plus, flags, NStr::IsBlank(), NCBI_THROW, revcomp(), s_GetReverseComplement(), NStr::ToUpper(), NStr::TruncateSpaces(), CSeqSearch::x_AddNucleotidePattern(), and CSeqSearch::x_IsJustTopStrand().

CBioseqGaps_CI()

CBioseqGaps_CI::CBioseqGaps_CI	(	const CSeq_entry_Handle &	entry_h,
		const Params &	params = Params()
	)

This constructor initializes the iterator.

Parameters

entry_h	This will iterate over all descendents of this entry.
params	Controls the behavior of the iterator. If not specified, a reasonable default will be used.

Definition at line 50 of file bioseqgaps_ci.cpp.

References CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_not_set, and NCBI_USER_THROW_FMT.

CDeflineGenerator() [1/3]

CDeflineGenerator::CDeflineGenerator ( const CDeflineGenerator &  )

private

CDeflineGenerator() [2/3]

CDeflineGenerator::CDeflineGenerator

(

const CSeq_entry_Handle &

tseh

)

Constructor.

Definition at line 131 of file create_defline.cpp.

References CDeflineGenerator::m_ConstructedFeatTree, CDeflineGenerator::m_InitializedFeatTree, CDeflineGenerator::m_TopSEH, and CDeflineGenerator::x_Init().

CDeflineGenerator() [3/3]

CDeflineGenerator::CDeflineGenerator

(

void

)

Constructor.

Definition at line 123 of file create_defline.cpp.

References CDeflineGenerator::m_ConstructedFeatTree, CDeflineGenerator::m_InitializedFeatTree, and CDeflineGenerator::x_Init().

CFastaOstream()

CFastaOstream::CFastaOstream

(

CNcbiOstream &

out

)

Definition at line 2713 of file sequence.cpp.

ChangeDeltaProteinToRawProtein()

bool CSeqTranslator::ChangeDeltaProteinToRawProtein ( CRef< CBioseq >  protein )

static

Definition at line 4086 of file sequence.cpp.

References CBioseq::IsAa(), CBioseq_Base::IsSetInst(), and CBioseq_Base::SetInst().

CLowQualityTextFsm()

CDeflineGenerator::CLowQualityTextFsm::CLowQualityTextFsm

(

void

)

Definition at line 4153 of file create_defline.cpp.

References CTextFsm< int >::AddWord(), and CTextFsm< int >::Prime().

CPatternInfo()

CSeqSearch::CPatternInfo::CPatternInfo ( const string &  name, const string &  sequence, Int2  cut_site  )

inline

constructor

Definition at line 1174 of file sequence.hpp.

CSeqSearch()

CSeqSearch::CSeqSearch	(	IClient *	client = 0,
		TSearchFlags	flags = fNoFlags
	)

constructors

Parameters

client	pointer to a client object (receives pattern match notifications)
flags	specify search flags

Definition at line 4797 of file sequence.cpp.

CSequenceAmbigTrimmer()

CSequenceAmbigTrimmer::CSequenceAmbigTrimmer	(	EMeaningOfAmbig	eMeaningOfAmbig,
		TFlags	fFlags = 0,
		const TTrimRuleVec &	vecTrimRules = GetDefaultTrimRules(),
		TSignedSeqPos	uMinSeqLen = 50
	)

This sets up the parameters for how this trimmer will act.

Parameters

eMeaningOfAmbig	This indicates exactly what ambiguous means (e.g. just "N" or do all ambiguous symbols count? )
fFlags	miscellaneous parameters to control this. See TFlags.
vecTrimRules	This indicates how trimming will occur. See TTrimRuleVec.
uMinSeqLen	Trimming tries to halt if the sequence becomes smaller than this size. It is possible for the resulting sequence to be below the uMinSeqLen size (or even trimmed to nothing), but the trimmer will at least try not to do that.

Definition at line 163 of file seq_trimmer.cpp.

References _ASSERT, ArraySize(), CSequenceAmbigTrimmer::eMeaningOfAmbig_AnyAmbig, CSequenceAmbigTrimmer::eMeaningOfAmbig_OnlyCompletelyUnknown, CSequenceAmbigTrimmer::m_arrNucAmbigLookupTable, CSequenceAmbigTrimmer::m_arrProtAmbigLookupTable, CSequenceAmbigTrimmer::m_eMeaningOfAmbig, CSequenceAmbigTrimmer::m_vecTrimRules, NCBI_USER_THROW_FMT, and CSequenceAmbigTrimmer::x_NormalizeVecTrimRules().

DECLARE_OPERATOR_BOOL()

CBioseqGaps_CI::DECLARE_OPERATOR_BOOL

(

m_bioseq_CI

)

DoTrim()

CSequenceAmbigTrimmer::EResult CSequenceAmbigTrimmer::DoTrim ( CBioseq_Handle &  bioseq_handle, CRangeCollection< TSeqPos > *  trimmed_ranges = nullptr  )

virtual

This trims the given bioseq, using params set in the CSequenceAmbigTrimmer constructor.

It will properly handle the annots and descs inside the bioseq, too, if requested.

Parameters

bioseq_handle	The bioseq to trim.
trimmed_ranges	The ranges trimmed by DoTrim will be added to this.

Returns

This returns how the trimming went. On error, an exception is thrown and the bioseq may be in an undefined state.

Definition at line 213 of file seq_trimmer.cpp.

References _ASSERT, CBioseq_Handle::eCoding_Iupac, CSequenceAmbigTrimmer::eResult_NoTrimNeeded, CSequenceAmbigTrimmer::eResult_SuccessfullyTrimmed, CSequenceAmbigTrimmer::fFlags_DoNotTrimBeginning, CSequenceAmbigTrimmer::fFlags_DoNotTrimEnd, CBioseq_Handle::GetBioseqLength(), CRangeCollection< Position >::GetCoveredLength(), CSequenceAmbigTrimmer::x_FindWhereToTrim(), CSequenceAmbigTrimmer::x_SliceBioseq(), CSequenceAmbigTrimmer::x_TestFlag(), and CSequenceAmbigTrimmer::x_TrimToNothing().

FindBestFrame() [1/2]

CCdregion::EFrame CSeqTranslator::FindBestFrame ( const CSeq_feat &  cds, CScope &  scope  )

static

Find "best" frame for a coding region.

"Best" frame has no internal stop codons.

Definition at line 4376 of file sequence.cpp.

Referenced by CEditSequence::AdjustFeatureLocations(), BOOST_AUTO_TEST_CASE(), CRetranslateCDS::GetCommand(), CEditCdsFrame::GetCommand(), ApplyCDSFrame::s_SetCDSFrame(), CMacroFunction_ApplyCDSFrame::s_SetCDSFrame(), CCleanup::SetBestFrame(), CMacroFunction_ApplyCDS::TheFunction(), UpdateFeat(), CFeaturePropagator::x_PropagateCds(), and CFeatureTableReader::xMoveCdRegions().

FindBestFrame() [2/2]

CCdregion::EFrame CSeqTranslator::FindBestFrame ( const CSeq_feat &  cds, CScope &  scope, bool &  ambiguous  )

static

Definition at line 4272 of file sequence.cpp.

References CSerialObject::Assign(), map_checker< Container >::begin(), eExtreme_Biological, CCdregion_Base::eFrame_not_set, CCdregion_Base::eFrame_one, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, map_checker< Container >::end(), NStr::Find(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), GetLength(), CSeq_feat_Base::GetLocation(), CSeqFeatData_Base::IsCdregion(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_feat_Base::IsSetData(), CCdregion_Base::IsSetFrame(), CSeq_feat_Base::IsSetLocation(), NPOS, NULL, prot, CSeq_feat_Base::SetData(), NStr::StartsWith(), and CSeqTranslator::Translate().

FindLatestSequence() [1/4]

CConstRef<CSeq_id> FindLatestSequence	(	const CSeq_id &	id,
		CScope &	scope
	)

Given a seq-id check its replace history and try to find the latest revision.

The function stops and returns NULL if it detects some strange conditions like an infinite recursion. If the bioseq contains no history information, the original id is returned.

Definition at line 763 of file sequence.cpp.

References CSeq_id_Handle::GetHandle(), CSeq_id_Handle::GetSeqId(), NULL, and x_FindLatestSequence().

Referenced by s_FindLatest().

FindLatestSequence() [2/4]

CConstRef<CSeq_id> FindLatestSequence	(	const CSeq_id &	id,
		CScope &	scope,
		const CTime &	tlim
	)

Check replace history up to the specified date.

Returns the latest bioseq up to the date or the original id if the bioseq contains no history or is already newer than the specified date.

Definition at line 774 of file sequence.cpp.

References CSeq_id_Handle::GetHandle(), CSeq_id_Handle::GetSeqId(), and x_FindLatestSequence().

FindLatestSequence() [3/4]

CSeq_id_Handle FindLatestSequence	(	const CSeq_id_Handle &	idh,
		CScope &	scope
	)

Definition at line 769 of file sequence.cpp.

References NULL, and x_FindLatestSequence().

FindLatestSequence() [4/4]

CSeq_id_Handle FindLatestSequence	(	const CSeq_id_Handle &	idh,
		CScope &	scope,
		const CTime &	tlim
	)

Definition at line 782 of file sequence.cpp.

References x_FindLatestSequence().

GenerateDefline() [1/6]

string CDeflineGenerator::GenerateDefline	(	const CBioseq &	bioseq,
		CScope &	scope,
		CSeqEntryIndex &	idx,
		TUserFlags	flags = 0
	)

Main method.

Definition at line 4098 of file create_defline.cpp.

References flags, CDeflineGenerator::GenerateDefline(), and CDeflineGenerator::m_Idx.

GenerateDefline() [2/6]

string CDeflineGenerator::GenerateDefline	(	const CBioseq &	bioseq,
		CScope &	scope,
		feature::CFeatTree &	ftree,
		TUserFlags	flags = 0
	)

Main method.

Definition at line 4138 of file create_defline.cpp.

References flags, CDeflineGenerator::GenerateDefline(), CDeflineGenerator::m_ConstructedFeatTree, CDeflineGenerator::m_Feat_Tree, and CDeflineGenerator::m_InitializedFeatTree.

GenerateDefline() [3/6]

string CDeflineGenerator::GenerateDefline	(	const CBioseq &	bioseq,
		CScope &	scope,
		TUserFlags	flags = 0
	)

Main method.

Definition at line 4125 of file create_defline.cpp.

References CScope::AddBioseq(), CScope::eExist_Get, flags, CDeflineGenerator::GenerateDefline(), and CScope::kPriority_Default.

GenerateDefline() [4/6]

string CDeflineGenerator::GenerateDefline	(	const CBioseq_Handle &	bsh,
		CSeqEntryIndex &	idx,
		TUserFlags	flags = 0
	)

Main method.

Definition at line 4086 of file create_defline.cpp.

References flags, CDeflineGenerator::GenerateDefline(), and CDeflineGenerator::m_Idx.

GenerateDefline() [5/6]

string CDeflineGenerator::GenerateDefline	(	const CBioseq_Handle &	bsh,
		feature::CFeatTree &	ftree,
		TUserFlags	flags = 0
	)

Main method.

Definition at line 4111 of file create_defline.cpp.

References flags, CDeflineGenerator::GenerateDefline(), CDeflineGenerator::m_ConstructedFeatTree, CDeflineGenerator::m_Feat_Tree, and CDeflineGenerator::m_InitializedFeatTree.

GenerateDefline() [6/6]

string CDeflineGenerator::GenerateDefline	(	const CBioseq_Handle &	bsh,
		TUserFlags	flags = 0
	)

Main method.

Definition at line 3909 of file create_defline.cpp.

References CSeqdesc_Base::e_User, ctll::empty(), CTempString::empty(), NStr::eNocase, CUser_object::eObjectType_AutodefOptions, CDeflineGenerator::fDoNotUseAutoDef, flags, CDeflineGenerator::fShowModifiers, CUser_object::GetObjectType(), CAutoDef::GetOneDefLine(), CSeqdesc_Base::GetUser(), NStr::HtmlDecode(), i, CAutoDefOptions::InitFromUserObject(), islower(), CDeflineGenerator::m_Feat_Tree, CDeflineGenerator::m_GpipeMode, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsAA, CDeflineGenerator::m_IsEST_STS_GSS, CDeflineGenerator::m_IsMap, CDeflineGenerator::m_IsNA, CDeflineGenerator::m_IsNC, CDeflineGenerator::m_IsNM, CDeflineGenerator::m_IsNR, CDeflineGenerator::m_IsNZ, CDeflineGenerator::m_IsPatent, CDeflineGenerator::m_IsPDB, CDeflineGenerator::m_IsSeg, CDeflineGenerator::m_IsTLS, CDeflineGenerator::m_IsTSA, CDeflineGenerator::m_IsWGS, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_MetaGenomeSource, CDeflineGenerator::m_MICompleteness, CDeflineGenerator::m_Reconstruct, CDeflineGenerator::m_TLSMaster, CDeflineGenerator::m_WGSMaster, NCBI_COMPLETENESS, NPOS, NULL, prefix, CRef< C, Locker >::Reset(), s_tpaPrefixList, s_TrimMainTitle(), CAutoDefModifierCombo::SetOptions(), CAutoDef::SetOptionsObject(), NStr::StartsWith(), str(), suffix, toupper(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), x_CleanAndCompress(), CDeflineGenerator::x_GetModifiers(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetBioSrcIdx(), CDeflineGenerator::x_SetFlags(), CDeflineGenerator::x_SetFlagsIdx(), CDeflineGenerator::x_SetPrefix(), CDeflineGenerator::x_SetSuffix(), CDeflineGenerator::x_SetTitleFromBioSrc(), CDeflineGenerator::x_SetTitleFromGPipe(), CDeflineGenerator::x_SetTitleFromMap(), CDeflineGenerator::x_SetTitleFromNC(), CDeflineGenerator::x_SetTitleFromNM(), CDeflineGenerator::x_SetTitleFromNR(), CDeflineGenerator::x_SetTitleFromPatent(), CDeflineGenerator::x_SetTitleFromPDB(), CDeflineGenerator::x_SetTitleFromProtein(), CDeflineGenerator::x_SetTitleFromProteinIdx(), CDeflineGenerator::x_SetTitleFromSegSeq(), and CDeflineGenerator::x_SetTitleFromWGS().

Referenced by CDeflineGenerator::GenerateDefline(), s_GetCdsSequence(), s_SetCloneInfo(), s_SetIdList(), CShowBlastDefline::x_FillDeflineAndId(), and CAlnGraphic::x_GetAlnInfo().

GetAccessionForGi()

string GetAccessionForGi	(	TGi	gi,
		CScope &	scope,
		EAccessionVersion	use_version = eWithAccessionVersion,
		EGetIdType	flags = 0
	)

Retrieve the accession for a given GI.

If no accession was found returns an empty string or throws CSeqIdFromHandleException depending on the flags. Id type in the flags is ignored, only VerifyId and ThrowOnError flags are checked.

Definition at line 686 of file sequence.cpp.

References CSeq_id_Base::e_Gi, eGetId_ForceAcc, eGetId_ThrowOnError, eGetId_VerifyId, eWithAccessionVersion, flags, GetId(), CSeq_id_Handle::GetSeqId(), CSeq_id::GetSeqIdString(), kEmptyStr, and NCBI_THROW.

Referenced by CDemoApp::GetIds(), ReplaceWellknownSeqs(), s_CheckQuals_cdregion(), s_ChrName(), s_CreateHistCommentString(), variation::CHgvsParser::s_SeqIdToHgvsStr(), CFeatureItem::x_AddQualProteinId(), and CAppHitFilter::x_LoadConstraints().

GetAccessionForId()

string GetAccessionForId	(	const objects::CSeq_id &	id,
		CScope &	scope,
		EAccessionVersion	use_version = eWithAccessionVersion,
		EGetIdType	flags = 0
	)

Retrieve the accession string for a Seq-id.

If no accession was found returns an empty string or throws CSeqIdFromHandleException depending on the flags. Id type in the flags is ignored, only VerifyId and ThrowOnError flags are checked.

Definition at line 708 of file sequence.cpp.

References eGetId_ForceAcc, eGetId_ThrowOnError, eGetId_VerifyId, eWithAccessionVersion, flags, GetId(), CSeq_id_Handle::GetSeqId(), CSeq_id::GetSeqIdString(), kEmptyStr, and NCBI_THROW.

Referenced by CLocMapper_Default::CLocMapper_Default(), SCompareAlignments::operator()(), SFlybaseCompareAlignments::operator()(), CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CGuiObjectInfoSeq_feat::x_GetAccession(), variation_ref::CHgvsParser::x_SeqIdToHgvsHeader(), CGff3Writer::x_WriteBioseqHandle(), and CSrcWriter::xGatherId().

GetAllFlags()

TFlags CFastaOstream::GetAllFlags ( void  ) const

inline

Definition at line 857 of file sequence.hpp.

GetBestCdsForMrna() [1/2]

CConstRef<CSeq_feat> GetBestCdsForMrna	(	const CSeq_feat &	mrna_feat,
		const CTSE_Handle &	tse,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2514 of file sequence.cpp.

References _ASSERT, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_mRNA, GetBestCdsForMrna(), CSeq_feat_Base::GetData(), CTSE_Handle::GetScope(), and CSeqFeatData::GetSubtype().

GetBestCdsForMrna() [2/2]

CConstRef<CSeq_feat> GetBestCdsForMrna	(	const CSeq_feat &	mrna_feat,
		CScope &	scope,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 1874 of file sequence.cpp.

References _ASSERT, CSeqFeatData_Base::e_Cdregion, eOverlap_CheckIntervals, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_mRNA, SAnnotSelector::ExcludeNamedAnnots(), fBestFeat_FavorLonger, fBestFeat_NoExpensive, fBestFeat_StrictMatch, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeq_id_Handle::GetHandle(), GetId(), CScope::GetIds(), CSeq_feat_Base::GetLocation(), CSeq_feat::GetNamedQual(), GetOverlappingFeatures(), CSeq_feat_Base::GetProduct(), CMappedFeat::GetProduct(), CSeqFeatData::GetSubtype(), CSeq_feat_Base::IsSetExt(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_Handle::IsSetProduct(), CBioseq_Handle::IsSynonym(), ITERATE, CConstRef< C, Locker >::Reset(), SAnnotSelector::SetFeatSubtype(), SAnnotSelector::SetOverlapIntervals(), and SAnnotSelector::SetResolveTSE().

Referenced by GetBestCdsForMrna(), GetBestOverlappingFeat(), and GetCdssForGene().

GetBestGeneForCds() [1/2]

CConstRef<CSeq_feat> GetBestGeneForCds	(	const CSeq_feat &	cds_feat,
		const CTSE_Handle &	tse,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2484 of file sequence.cpp.

References _ASSERT, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, GetBestGeneForCds(), CSeq_feat_Base::GetData(), CTSE_Handle::GetScope(), and CSeqFeatData::GetSubtype().

GetBestGeneForCds() [2/2]

CConstRef<CSeq_feat> GetBestGeneForCds	(	const CSeq_feat &	cds_feat,
		CScope &	scope,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2128 of file sequence.cpp.

References _ASSERT, CSeqFeatData_Base::e_Gene, eOverlap_Contained, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_cdregion, fBestFeat_NoExpensive, fBestFeat_StrictMatch, GetBestGeneForMrna(), GetBestMrnaForCds(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CSeq_feat::GetGeneXref(), CGene_ref::GetLabel(), CSeq_feat_Base::GetLocation(), GetOverlappingFeatures(), CSeqFeatData::GetSubtype(), CGene_ref::IsSuppressed(), and ITERATE.

Referenced by GetBestGeneForCds(), and GetBestOverlappingFeat().

GetBestGeneForMrna() [1/2]

CConstRef<CSeq_feat> GetBestGeneForMrna	(	const CSeq_feat &	mrna_feat,
		const CTSE_Handle &	tse,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2469 of file sequence.cpp.

References _ASSERT, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, GetBestGeneForMrna(), CSeq_feat_Base::GetData(), CTSE_Handle::GetScope(), and CSeqFeatData::GetSubtype().

GetBestGeneForMrna() [2/2]

CConstRef<CSeq_feat> GetBestGeneForMrna	(	const CSeq_feat &	mrna_feat,
		CScope &	scope,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2040 of file sequence.cpp.

References _ASSERT, CSeqFeatData_Base::e_Gene, eOverlap_Contained, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_mRNA, fBestFeat_FavorLonger, fBestFeat_StrictMatch, CSeq_feat_Base::GetData(), CSeq_feat_Base::GetDbxref(), CSeqFeatData_Base::GetGene(), CSeq_feat::GetGeneXref(), CGene_ref::GetLabel(), CSeq_feat_Base::GetLocation(), GetOverlappingFeatures(), CSeqFeatData::GetSubtype(), CSeq_feat_Base::IsSetDbxref(), CGene_ref::IsSuppressed(), and ITERATE.

Referenced by GetBestGeneForCds(), GetBestGeneForMrna(), and GetBestOverlappingFeat().

GetBestMrnaForCds() [1/2]

CConstRef<CSeq_feat> GetBestMrnaForCds	(	const CSeq_feat &	cds_feat,
		const CTSE_Handle &	tse,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2499 of file sequence.cpp.

References _ASSERT, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_mRNA, GetBestMrnaForCds(), CSeq_feat_Base::GetData(), CTSE_Handle::GetScope(), and CSeqFeatData::GetSubtype().

GetBestMrnaForCds() [2/2]

CConstRef<CSeq_feat> GetBestMrnaForCds	(	const CSeq_feat &	cds_feat,
		CScope &	scope,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 1609 of file sequence.cpp.

References _ASSERT, CSeqFeatData_Base::e_Rna, eOverlap_CheckIntRev, eOverlap_SubsetRev, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_mRNA, SAnnotSelector::ExcludeNamedAnnots(), fBestFeat_FavorLonger, fBestFeat_NoExpensive, fBestFeat_StrictMatch, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), CSeq_id_Handle::GetHandle(), GetId(), CScope::GetIds(), CSeq_feat_Base::GetLocation(), CSeq_feat::GetNamedQual(), CMappedFeat::GetOriginalFeature(), GetOverlappingFeatures(), CSeq_feat_Base::GetProduct(), CSeqFeatData::GetSubtype(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), CSeq_feat_Base::IsSetExt(), CSeq_feat_Base::IsSetProduct(), CBioseq_Handle::IsSynonym(), ITERATE, kRibosomalSlippageText, CSeq_id::Match(), CConstRef< C, Locker >::Reset(), SAnnotSelector::SetFeatSubtype(), SAnnotSelector::SetOverlapIntervals(), and SAnnotSelector::SetResolveTSE().

Referenced by GetBestGeneForCds(), GetBestMrnaForCds(), and GetBestOverlappingFeat().

GetBestOverlapForSNP() [1/2]

CConstRef<CSeq_feat> GetBestOverlapForSNP	(	const CSeq_feat &	snp_feat,
		CSeqFeatData::E_Choice	type,
		CScope &	scope,
		bool	search_both_strands = true
	)

Get the best overlapping feature for a SNP (variation) feature.

Parameters

snp_feat	SNP feature object
type	type of overlapping feature
scope
search_both_strands	search is performed on both strands, starting with the one specified by the feature's location.

Returns

the overlapping fetaure or NULL if not found

Definition at line 1345 of file sequence.cpp.

References CSeqFeatData::eSubtype_any, and x_GetBestOverlapForSNP().

Referenced by GetBestOverlappingFeat(), and CTestBMApp::Run().

GetBestOverlapForSNP() [2/2]

CConstRef<CSeq_feat> GetBestOverlapForSNP	(	const CSeq_feat &	snp_feat,
		CSeqFeatData::ESubtype	subtype,
		CScope &	scope,
		bool	search_both_strands = true
	)

Get the best overlapping feature for a SNP (variation)

Parameters

snp_feat	SNP feature object
subtype	subtype of overlapping feature
scope
search_both_strands	search is performed on both strands, starting with the one specified by the feature's location.

Returns

the overlapping fetaure or NULL if not found

Definition at line 1355 of file sequence.cpp.

References CSeqFeatData::GetTypeFromSubtype(), and x_GetBestOverlapForSNP().

GetBestOverlappingFeat() [1/4]

CConstRef<CSeq_feat> GetBestOverlappingFeat	(	const CSeq_feat &	feat,
		CSeqFeatData::E_Choice	feat_type,
		sequence::EOverlapType	overlap_type,
		CScope &	scope,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2347 of file sequence.cpp.

References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Rna, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, GetBestOverlappingFeat(), and CSeq_feat_Base::GetLocation().

GetBestOverlappingFeat() [2/4]

CConstRef<CSeq_feat> GetBestOverlappingFeat	(	const CSeq_feat &	feat,
		CSeqFeatData::ESubtype	feat_type,
		sequence::EOverlapType	overlap_type,
		CScope &	scope,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2386 of file sequence.cpp.

References CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_variation, GetBestCdsForMrna(), GetBestGeneForCds(), GetBestGeneForMrna(), GetBestMrnaForCds(), GetBestOverlapForSNP(), GetBestOverlappingFeat(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), and CSeqFeatData::GetSubtype().

GetBestOverlappingFeat() [3/4]

CConstRef<CSeq_feat> GetBestOverlappingFeat	(	const CSeq_loc &	loc,
		CSeqFeatData::E_Choice	feat_type,
		EOverlapType	overlap_type,
		CScope &	scope,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

See the note above on 'overlap_type' meaning.

Definition at line 1208 of file sequence.cpp.

References CSeqFeatData::eSubtype_any, fBestFeat_FavorLonger, and GetOverlappingFeatures().

Referenced by GetBestOverlappingFeat(), GetCdssForGene(), GetmRNAforCDS(), GetMrnasForGene(), GetOverlappingCDS(), GetOverlappingGene(), GetOverlappingmRNA(), GetOverlappingOperon(), GetOverlappingPub(), GetOverlappingSource(), and GetSourceFeatForProduct().

GetBestOverlappingFeat() [4/4]

CConstRef<CSeq_feat> GetBestOverlappingFeat	(	const CSeq_loc &	loc,
		CSeqFeatData::ESubtype	feat_type,
		EOverlapType	overlap_type,
		CScope &	scope,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

See the note above on 'overlap_type' meaning.

Definition at line 1230 of file sequence.cpp.

References fBestFeat_FavorLonger, GetOverlappingFeatures(), and CSeqFeatData::GetTypeFromSubtype().

GetBioseqFromSeqLoc()

CBioseq_Handle GetBioseqFromSeqLoc	(	const CSeq_loc &	loc,
		CScope &	scope,
		CScope::EGetBioseqFlag	flag = CScope::eGetBioseq_Loaded
	)

Retrieve the Bioseq Handle from a location.

location refers to a single bioseq: return the bioseq location referes to multiple bioseqs: if parts of a segmentd bioseq, returns the segmentd bioseq. otherwise, return the first bioseq that could be found (first localy then, if flag is eGetBioseq_All, remote)

Definition at line 307 of file sequence.cpp.

References CScope::eGetBioseq_All, CScope::eGetBioseq_Loaded, CScope::GetBioseqHandle(), GetId(), GetParentForPart(), IsOneBioseq(), and CBioseq_Handle::Reset().

Referenced by CFlatFileGenerator::Generate(), GetGeneForFeature(), GetProductName(), CFlatFileGenerator::GetSeqFeatText(), GetStop(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), s_GetProductName(), sGetCdsProductName(), CFlatGatherer::x_GatherCDSReferences(), CFlatGatherer::x_GatherReferences(), CFlatGatherer::x_GatherReferencesIdx(), CFlatFeatureRetrieveJob::x_Run(), and CBioseqContext::x_SetMapper().

GetBioSource() [1/2]

const CBioSource* GetBioSource

(

const CBioseq &

bioseq

)

Retrieve the BioSource object for a given bioseq handle.

If the supplied sequence does not have a MolInfo associated with it, this will return NULL

Definition at line 104 of file sequence.cpp.

References ITERATE, and NULL.

Referenced by CopyOrg(), fg::GetGeneticCode(), IAlignRowHandle::GetOrgLabel(), IAlignRowHandle::GetTaxonomy(), variation::IsMitochondrion(), CMakeBadSpecificHostTable::MakeTable(), CTreeBuilderJob::x_CreateProjectItems(), CSparseAln::x_GetGenCode(), CDeflineGenerator::x_GetModifiers(), and CNewCleanup_imp::x_RemoveSingleStrand().

GetBioSource() [2/2]

const CBioSource* GetBioSource

(

const CBioseq_Handle &

handle

)

Definition at line 115 of file sequence.cpp.

References CSeqdesc_Base::e_Source, CSeqdesc_Base::GetSource(), CBioseq_Handle::GetTopLevelEntry(), and NULL.

GetBioSourceForBioseq()

const CBioSource* GetBioSourceForBioseq

(

const CBioseq_Handle &

bsh

)

Find a BioSource for the given Bioseq: If it's a protein then look for the source feature of the product.

Otherwise find a source descriptor for the sequence. Otherwise, try to find a source feature for the sequence. Return nullptr if we still turn up empty.

Definition at line 220 of file sequence.cpp.

References CSeqFeatData_Base::e_Biosrc, CSeqdesc_Base::e_Source, CSeqFeatData_Base::GetBiosrc(), CSeq_feat_Base::GetData(), CMappedFeat::GetOriginalFeature(), CSeqdesc_Base::GetSource(), GetSourceFeatForProduct(), and CBioseq_Handle::IsAa().

Referenced by GetOrg_refForBioseq(), and CGff3Writer::xAssignSourceAttributesBioSource().

GetCDSForProduct() [1/2]

const CSeq_feat* GetCDSForProduct	(	const CBioseq &	product,
		CScope *	scope
	)

Get the encoding CDS feature of a given protein sequence.

Definition at line 2549 of file sequence.cpp.

References CScope::GetBioseqHandle().

Referenced by CValidError_bioseq::CdError(), CConvertProtToImp::Convert(), CNewCleanup_imp::CreateMissingMolInfo(), IEditingActionFeat::FindRelated(), CEditingActionFeatGeneLocus::FindRelated(), CProductColumn::GetApplyObjects(), CCodonStartColumn::GetApplyObjects(), NMacroUtil::GetLocusTagFromProtRef(), GetNucleotideParent(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), GetSourceFeatForProduct(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), IEditingAction::GetUpdateMRNAProductNameCmd(), CLocationConstraintMatcher::Match(), CNewCleanup_imp::ResynchProteinPartials(), s_GetProtApplyObjectsFeatures(), s_GetProteinName(), CMacroFunction_UpdateProteinSeqs::TheFunction(), UpdatemRNAProduct(), CValidError_bioseq::ValidateRawConst(), CCmdFeatIdXrefsFromQualifiers::x_CreateActionCmd(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), CFlatGatherer::x_GatherCDSReferences(), CDBSourceItem::x_GatherInfo(), x_GetDivisionProc(), x_GetDivisionProcIdx(), x_GetSourceFeatViaCDS(), CMacroFunction_ParsedText::x_GetSpecialField(), CCdregionValidator::x_ValidateCommonProduct(), and CSingleFeatValidator::x_ValidateGeneXRef().

GetCDSForProduct() [2/2]

const CSeq_feat* GetCDSForProduct

(

const CBioseq_Handle &

product

)

Definition at line 2558 of file sequence.cpp.

References f(), and GetMappedCDSForProduct().

GetCdssForGene() [1/2]

void GetCdssForGene	(	const CSeq_feat &	gene_feat,
		const CTSE_Handle &	tse,
		list< CConstRef< CSeq_feat > > &	cds_feats,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2538 of file sequence.cpp.

References _ASSERT, CSeqFeatData::eSubtype_gene, GetCdssForGene(), CSeq_feat_Base::GetData(), CTSE_Handle::GetScope(), and CSeqFeatData::GetSubtype().

GetCdssForGene() [2/2]

void GetCdssForGene	(	const CSeq_feat &	gene_feat,
		CScope &	scope,
		list< CConstRef< CSeq_feat > > &	cds_feats,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2318 of file sequence.cpp.

References _ASSERT, eOverlap_Subset, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, GetBestCdsForMrna(), GetBestOverlappingFeat(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), GetMrnasForGene(), CSeqFeatData::GetSubtype(), and ITERATE.

Referenced by GetCdssForGene().

GetClient()

const IClient* CSeqSearch::GetClient ( void  ) const

inline

Get / Set client.

Definition at line 1250 of file sequence.hpp.

References CSeqSearch::m_Client.

GetCutSite()

Int2 CSeqSearch::CPatternInfo::GetCutSite ( void  ) const

inline

Definition at line 1183 of file sequence.hpp.

References CSeqSearch::CPatternInfo::m_CutSite.

GetDefaultTrimRules()

const CSequenceAmbigTrimmer::TTrimRuleVec & CSequenceAmbigTrimmer::GetDefaultTrimRules ( void  )

static

This returns a reasonable default for trimming rules.

Definition at line 156 of file seq_trimmer.cpp.

References CSafeStatic< T, Callbacks >::Get(), and NULL.

GetErrCodeString()

const char * CSeqIdFromHandleException::GetErrCodeString ( void  ) const

overridevirtual

Definition at line 406 of file sequence.cpp.

References CSeqIdFromHandleException::eNoSynonyms, CSeqIdFromHandleException::eRequestedIdNotFound, and CException::GetErrCodeString().

GetGapMode()

EGapMode CFastaOstream::GetGapMode ( void  ) const

inline

Definition at line 862 of file sequence.hpp.

GetGapModText()

void CFastaOstream::GetGapModText ( const CSeq_gap &  seq_gap, SGapModText &  out_gap_mod_text  )

static

Given a CSeq_gap object, this outputs the Gap information.

Parameters

seq_gap	This is the seq_gap information we're using to figure out the gap mod text
out_gap_mod_text	This holds the result.

Definition at line 3483 of file sequence.cpp.

References CSeq_gap_Base::CanGetLinkage(), CSeq_gap_Base::CanGetLinkage_evidence(), CLinkage_evidence_Base::CanGetType(), CSeq_gap_Base::CanGetType(), CSeq_gap_Base::eLinkage_linked, CLinkage_evidence_Base::eType_align_genus, CLinkage_evidence_Base::eType_align_trnscpt, CLinkage_evidence_Base::eType_align_xgenus, CSeq_gap_Base::eType_centromere, CSeq_gap_Base::eType_clone, CLinkage_evidence_Base::eType_clone_contig, CSeq_gap_Base::eType_contamination, CSeq_gap_Base::eType_contig, CSeq_gap_Base::eType_fragment, CSeq_gap_Base::eType_heterochromatin, CLinkage_evidence_Base::eType_map, CLinkage_evidence_Base::eType_other, CSeq_gap_Base::eType_other, CLinkage_evidence_Base::eType_paired_ends, CLinkage_evidence_Base::eType_pcr, CLinkage_evidence_Base::eType_proximity_ligation, CSeq_gap_Base::eType_repeat, CSeq_gap_Base::eType_scaffold, CSeq_gap_Base::eType_short_arm, CLinkage_evidence_Base::eType_strobe, CSeq_gap_Base::eType_telomere, CSeq_gap_Base::eType_unknown, CLinkage_evidence_Base::eType_unspecified, CLinkage_evidence_Base::eType_within_clone, CFastaOstream::SGapModText::gap_linkage_evidences, CFastaOstream::SGapModText::gap_type, CSeq_gap_Base::GetLinkage(), CSeq_gap_Base::GetLinkage_evidence(), CLinkage_evidence_Base::GetType(), CSeq_gap_Base::GetType(), NStr::IntToString(), CSeq_gap_Base::IsSetLinkage_evidence(), and ITERATE.

Referenced by s_NewGapItem(), CBioseqIndex::x_InitGaps(), and CFastaOstream::x_WriteSequence().

GetGeneForFeature()

CConstRef<CSeq_feat> GetGeneForFeature	(	const CSeq_feat &	feat,
		CScope &	scope
	)

Finds gene for feature, but obeys SeqFeatXref directives.

Definition at line 1529 of file sequence.cpp.

Referenced by AddExceptionsToShortIntron(), CAutoDefFeatureClause::AddGene(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CDiscrepancyContext::GeneForFeature(), CGeneCache::GetGeneFromCache(), GetLocusTagForFeature(), CFeatureSeqTableColumnBase::GetRelatedGeneApplyObjects(), GetTargetedLocusName(), CBioseqEditor::OnDeleteSelection(), CMacroFunction_ConvertLocStrand::TheFunction(), CMacroFunction_ConvertLocType::TheFunction(), CCleanupApp::x_FixCDS(), CValidErrorFormat::x_FormatECNumberForSubmitterReport(), and CValidErrorFormat::x_GetLocusTag().

GetGiForAccession()

TGi GetGiForAccession	(	const string &	acc,
		CScope &	scope,
		EGetIdType	flags = 0
	)

Given an accession string retrieve the GI id.

If no GI was found returns 0 or throws CSeqIdFromHandleException depending on the flags. Id type in the flags is ignored, only VerifyId and ThrowOnError flags are checked.

Definition at line 638 of file sequence.cpp.

References CSeq_id::AvoidGi(), eGetId_ForceGi, eGetId_ThrowOnError, eGetId_VerifyId, flags, CSeq_id_Handle::GetGi(), GetId(), CSeq_id::GetTextseq_Id(), CSeq_id_Handle::IsGi(), NCBI_THROW, and ZERO_GI.

Referenced by BOOST_AUTO_TEST_CASE(), CSequenceDataTester::x_Init(), and CAppHitFilter::x_LoadConstraints().

GetGiForId()

TGi GetGiForId	(	const objects::CSeq_id &	id,
		CScope &	scope,
		EGetIdType	flags = 0
	)

Given a Seq-id retrieve the corresponding GI.

If no GI was found returns 0 or throws CSeqIdFromHandleException depending on the flags. Id type in the flags is ignored, only VerifyId and ThrowOnError flags are checked.

Definition at line 668 of file sequence.cpp.

References CSeq_id::AvoidGi(), eGetId_ForceGi, eGetId_ThrowOnError, eGetId_VerifyId, flags, CSeq_id_Handle::GetGi(), GetId(), CSeq_id_Handle::IsGi(), NCBI_THROW, and ZERO_GI.

Referenced by fta_get_gi_for_seq_id(), CSeqIdListSet::GetGiList(), CSeqLocListSet::GetGiList(), CLocationListCtrl::GetIdFromForm(), CBinsTrack::InitHTMLActiveArea(), CVarTrack::InitHTMLActiveArea(), CSeqUtils::isTopLevel(), CBinsGlyph::x_BuildNonEmptyBinList(), CGeneMarkerGlyph::x_BuildSignatures(), and CCreateGeneModelTask::x_GetCommand().

GetId() [1/5]

CSeq_id_Handle GetId	(	const CBioseq &	seq,
		EGetIdType	type = eGetId_Default
	)

Return a selected ID type from a Bioseq Arguments (except 'seq') and behavior is the same as of GetId(const CBioseq_Handle& seq, ...).

Definition at line 535 of file sequence.cpp.

References CBioseq_Base::GetId().

Referenced by GetAccessionForGi(), GetAccessionForId(), GetBestCdsForMrna(), GetBestMrnaForCds(), GetBioseqFromSeqLoc(), GetGiForAccession(), GetGiForId(), GetId(), and GetProteinName().

GetId() [2/5]

CSeq_id_Handle GetId	(	const CBioseq::TId &	id,
		EGetIdType	type = eGetId_Default
	)

Return a selected ID type from a set of Seq-ids Arguments (except 'id') and behavior is the same as of GetId(const CSeq_id& id, ...).

Definition at line 541 of file sequence.cpp.

References CSeq_id_Handle::GetHandle(), ITERATE, and x_GetId().

GetId() [3/5]

CSeq_id_Handle GetId	(	const CBioseq_Handle &	handle,
		EGetIdType	type = eGetId_Default
	)

Return a selected ID type for a given bioseq handle.

This function will try to use the most efficient method possible to determine which ID fulfills the requested parameter. This version will call sequence::GetId() with the bioseq handle's seq-id.

Parameters

id	Source id to evaluate
scope	Scope for seq-id resolution.
type	Type of ID to return

Returns

A requested seq-id. Depending on the flags set in 'type' this function can verify if the requested ID exists in the scope and throw CSeqIdFromHandleException if the request cannot be satisfied.

Definition at line 621 of file sequence.cpp.

References _ASSERT, eGetId_ThrowOnError, CBioseq_Handle::GetId(), NCBI_THROW, and x_GetId().

GetId() [4/5]

CSeq_id_Handle GetId	(	const CSeq_id &	id,
		CScope &	scope,
		EGetIdType	type = eGetId_Default
	)

Return a selected ID type for a seq-id.

This function will try to use the most efficient method possible to determine which ID fulfills the requested parameter. The following logic is used:

• For seq-id type eGetId_HandleDefault, the original seq-id is returned. This satisfies the condition of returning a bioseq-handle's seq-id if sequence::GetId() is applied to a CBioseq_Handle.
• For seq-id type eGetId_ForceAcc, the returned set of seq-ids will first be evaluated for a "best" id (which, given seq-id scoring, will be a textseq-id if one exists). If the returned best ID is a textseq-id, this id will be returned. Otherwise, an exception is thrown or an empty handle returned.
• For seq-id type eGetId_ForceGi, the returned set of IDs is scanned for an ID of type gi. If this is found, it is returned; otherwise, an exception is thrown or an empty handle returned. If the supplied ID is already a gi and eGetId_VerifyId flag is not set, no work is done.

Parameters

id	Source id to evaluate
scope	Scope for seq-id resolution.
type	Type of ID to return

Returns

A requested seq-id. Depending on the flags set in 'type' this function can verify if the requested ID exists in the scope and throw CSeqIdFromHandleException if the request cannot be satisfied.

Definition at line 552 of file sequence.cpp.

References CSeq_id_Handle::GetHandle(), and GetId().

GetId() [5/5]

CSeq_id_Handle GetId	(	const CSeq_id_Handle &	id,
		CScope &	scope,
		EGetIdType	type = eGetId_Default
	)

Return a selected ID type for a seq-id handle.

Arguments (except 'id') and behavior is the same as of GetId(const CSeq_id& id, ...).

Definition at line 558 of file sequence.cpp.

References _ASSERT, CSeq_id_Base::e_General, eGetId_Canonical, eGetId_ForceAcc, eGetId_ForceGi, eGetId_ThrowOnError, eGetId_TypeMask, eGetId_VerifyId, ERR_POST, CScope::GetAccVer(), CScope::GetGi(), CSeq_id_Handle::GetGiHandle(), CScope::GetIds(), CSeq_id_Handle::GetSeqId(), CSeq_id_Base::IsGeneral(), CSeq_id_Handle::IsGi(), NCBI_THROW, CSeq_id::PreferAccessionOverGi(), CSeq_id_Handle::Reset(), CSeq_id_Handle::Which(), x_GetId(), and ZERO_GI.

GetMappedCDSForProduct()

CMappedFeat GetMappedCDSForProduct

(

const CBioseq_Handle &

product

)

Definition at line 2568 of file sequence.cpp.

References CSeqFeatData_Base::e_Cdregion, fi, and CBioseq_Handle::GetTSE_Handle().

Referenced by ChangeFeat(), CGeneFinder::GetAssociatedGeneInfo(), GetCDSForProduct(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), and CDeflineGenerator::x_SetTitleFromProtein().

GetMappedmRNAForProduct()

CMappedFeat GetMappedmRNAForProduct

(

const CBioseq_Handle &

product

)

Definition at line 2642 of file sequence.cpp.

References CSeqFeatData::eSubtype_mRNA, and fi.

Referenced by CFlatGatherer::x_GatherFeatures(), and CFlatGatherer::x_GatherFeaturesIdx().

GetMask()

CConstRef< CSeq_loc > CFastaOstream::GetMask

(

EMaskType

type

)

const

Definition at line 3444 of file sequence.cpp.

References CFastaOstream::eSoftMask, CFastaOstream::m_HardMask, and CFastaOstream::m_SoftMask.

GetMolInfo() [1/2]

const CMolInfo* GetMolInfo

(

const CBioseq &

bioseq

)

Retrieve the MolInfo object for a given bioseq handle.

If the supplied sequence does not have a MolInfo associated with it, this will return NULL

Definition at line 284 of file sequence.cpp.

References CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), ITERATE, and NULL.

Referenced by AddDefaultSentinelFeats(), CAlignCollapser::GetCollapsedAlgnments(), variation::CVariationUtil::GetMolType(), CAlignCollapser::GetOnlyOtherAlignments(), GetSequenceType(), CSGUtils::IsmRNA(), CGuiObjectInfoSeq_align::IsPolyA(), CDiscrepancyPanel::OnListClk(), CFeatureGenerator::SImplementation::SMapper::SMapper(), and CDeflineGenerator::x_GetModifiers().

GetMolInfo() [2/2]

const CMolInfo* GetMolInfo

(

const CBioseq_Handle &

handle

)

Definition at line 295 of file sequence.cpp.

References CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::GetMolinfo(), and NULL.

GetmRNAforCDS()

CConstRef<CSeq_feat> GetmRNAforCDS	(	const CSeq_feat &	cds,
		CScope &	scope
	)

GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS.

Parameters

cds	The feature for which the mRNA to be found
scope	The scope

Returns

CConstRef<CSeq_feat> for new mRNA (will be NULL if none is found)

Definition at line 1261 of file sequence.cpp.

Referenced by CAdjustForConsensusSpliceSite::AdjustmRNAandExonEnds(), CAdjustForConsensusSpliceSite::AdjustmRNAandExonFeatures(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CCleanup::ExtendToStopIfShortAndNotPartial(), CTruncateCDS::GetCommand(), IEditingAction::GetUpdateMRNAProductNameCmd(), CBulkCDS::GetUpdateMRNAProductNameCmd(), UpdatemRNAProduct(), CCleanup::WGSCleanup(), CCleanupApp::x_FixCDS(), and CCdregionValidator::x_ValidateParentPartialness().

GetmRNAForProduct() [1/2]

const CSeq_feat* GetmRNAForProduct	(	const CBioseq &	product,
		CScope *	scope
	)

Get the encoding mRNA feature of a given mRNA (cDNA) bioseq.

Definition at line 2617 of file sequence.cpp.

References CScope::GetBioseqHandle().

Referenced by CNewCleanup_imp::CreateMissingMolInfo(), and GetNucleotideParent().

GetmRNAForProduct() [2/2]

const CSeq_feat* GetmRNAForProduct

(

const CBioseq_Handle &

product

)

Definition at line 2626 of file sequence.cpp.

References CSeqFeatData::eSubtype_mRNA, fi, and SAnnotSelector::SetByProduct().

GetMrnasForGene() [1/2]

void GetMrnasForGene	(	const CSeq_feat &	gene_feat,
		const CTSE_Handle &	tse,
		list< CConstRef< CSeq_feat > > &	mrna_feats,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2528 of file sequence.cpp.

References _ASSERT, CSeqFeatData::eSubtype_gene, CSeq_feat_Base::GetData(), GetMrnasForGene(), CTSE_Handle::GetScope(), and CSeqFeatData::GetSubtype().

GetMrnasForGene() [2/2]

void GetMrnasForGene	(	const CSeq_feat &	gene_feat,
		CScope &	scope,
		list< CConstRef< CSeq_feat > > &	mrna_feats,
		TBestFeatOpts	opts = fBestFeat_Defaults,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Definition at line 2195 of file sequence.cpp.

References _ASSERT, Compare(), eContains, eOverlap_Contains, eSame, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, fCompareOverlapping, GetBestOverlappingFeat(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetDbxref(), CSeq_feat_Handle::GetDbxref(), CSeqFeatData_Base::GetGene(), CSeq_feat::GetGeneXref(), CGene_ref::GetLabel(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetLocation(), CMappedFeat::GetOriginalFeature(), CAnnotTypes_CI::GetSize(), CSeqFeatData::GetSubtype(), SAnnotSelector::IncludeFeatSubtype(), CSeq_feat_Base::IsSetDbxref(), CSeq_feat_Handle::IsSetDbxref(), CGene_ref::IsSuppressed(), ITERATE, CFeat_CI::Rewind(), SAnnotSelector::SetAdaptiveDepth(), and SAnnotSelector::SetResolveTSE().

Referenced by GetCdssForGene(), and GetMrnasForGene().

GetName()

const string& CSeqSearch::CPatternInfo::GetName ( void  ) const

inline

Definition at line 1181 of file sequence.hpp.

References CSeqSearch::CPatternInfo::m_Name.

GetNucleotideParent() [1/2]

const CBioseq* GetNucleotideParent	(	const CBioseq &	product,
		CScope *	scope
	)

Get the encoding nucleotide sequnce of a protein.

Definition at line 2660 of file sequence.cpp.

References CScope::GetBioseqHandle(), and CBioseq_Handle::GetCompleteBioseq().

Referenced by GetModelEvidance(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneIdForProduct(), and CLocusItem::x_SetDate().

GetNucleotideParent() [2/2]

CBioseq_Handle GetNucleotideParent

(

const CBioseq_Handle &

product

)

Definition at line 2669 of file sequence.cpp.

References CScope::GetBioseqHandle(), GetCDSForProduct(), CBioseq_Handle::GetInst(), CSeq_feat_Base::GetLocation(), GetmRNAForProduct(), CBioseq_Handle::GetScope(), and CSeq_inst::IsAa().

GetOrg_ref()

const COrg_ref& GetOrg_ref

(

const CBioseq_Handle &

handle

)

Return the org-ref associated with a given sequence.

This will throw a CException if there is no org-ref associated with the sequence

Definition at line 264 of file sequence.cpp.

References eUnknown, GetOrg_refOrNull(), and NCBI_THROW.

Referenced by BOOST_AUTO_TEST_CASE(), CProteinAlignText::CProteinAlignText(), CProSplign::CImplementation::FindGlobalAlignment_stage1(), CScoreBuilder::GetBlastScoreProtToNucl(), CSequenceTrack::GetTooltip(), CGuiObjectInfoComponent::GetToolTip(), s_GetGeneticCode(), s_GetSplicedSegIdentityMismatch(), CFeatureGenerator::SImplementation::x_ConstructRnaName(), CTreeBuilderJob::x_CreateProjectItems(), CAlnVecRow::x_GetDescrTooltip(), CAlignSeqTableModel::x_GetOrganism(), CSFTranslationJob::x_InitGeneticCode(), and CPhyTreeFormatter::x_InitTreeFeatures().

GetOrg_refForBioseq()

const COrg_ref* GetOrg_refForBioseq

(

const CBioseq_Handle &

bsh

)

Find an Org-ref for the given Bioseq: If it's a protein then look on the source feature of the product.

Otherwise find a source descriptor for the sequence. Otherwise, try to find a source feature for the sequence. Return nullptr if we still turn up empty.

Definition at line 211 of file sequence.cpp.

References GetBioSourceForBioseq().

GetOrg_refForProduct()

void GetOrg_refForProduct	(	const CBioseq_Handle &	bsh,
		const COrg_ref *	pOrgRef
	)

Definition at line 194 of file sequence.cpp.

References GetSourceFeatForProduct(), and CBioseq_Handle::IsAa().

GetOrg_refOrNull()

const COrg_ref* GetOrg_refOrNull

(

const CBioseq_Handle &

handle

)

Return the pointer to org-ref associated with a given sequence or null if there is no org-ref associated with the sequence.

Definition at line 245 of file sequence.cpp.

References CSeqdesc_Base::e_Org, CSeqdesc_Base::e_Source, CSeqdesc_Base::GetOrg(), CBioSource_Base::GetOrg(), CSeqdesc_Base::GetSource(), CSeqdesc_Base::IsOrg(), CSeqdesc_Base::IsSource(), and types.

Referenced by CFeatureGenerator::ConvertLocToAnnot(), GetOrg_ref(), GetTaxId(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), and CSparseAln::x_GetGenCode().

GetOverlappingCDS()

CConstRef<CSeq_feat> GetOverlappingCDS	(	const CSeq_loc &	loc,
		CScope &	scope
	)

Definition at line 1579 of file sequence.cpp.

References eOverlap_Contained, CSeqFeatData::eSubtype_cdregion, and GetBestOverlappingFeat().

Referenced by CSequenceEditingEventHandler::CombineSelectedGenesIntoPseudogenes(), CPeptideValidator::CPeptideValidator(), CCleanup::GetProteinLocationFromNucleotideLocation(), s_MoveProteinSpecificFeats(), and CImpFeatValidator::Validate().

GetOverlappingFeatures()

void GetOverlappingFeatures	(	const CSeq_loc &	loc,
		CSeqFeatData::E_Choice	feat_type,
		CSeqFeatData::ESubtype	feat_subtype,
		EOverlapType	overlap_type,
		TFeatScores &	feats,
		CScope &	scope,
		const TBestFeatOpts	opts = 0,
		CGetOverlappingFeaturesPlugin *	plugin = NULL
	)

Find all features overlapping the location.

Features and corresponding scores are stored in the 'feats' vector. The scores are calculated as difference between the input location and each feature's location. NOTE: 'overlap_type' defines how the location must be related to the feature. For eOverlap_Subset, eOverlap_SubsetRev, eOverlap_CheckIntervals, eOverlap_CheckIntRev and eOverlap_Interval the relationship is reversed. E.g. with eOverlap_Contains, the location will contain the feature, but with eOverlap_Subset the feature will be defined on a subset of the location.

Definition at line 945 of file sequence.cpp.

References _DEBUG_ARG, _TRACE, CSeq_loc::Assign(), CSeq_loc::CheckId(), Compare(), ConstRef(), eContains, eExtreme_Positional, eNa_strand_plus, eNa_strand_unknown, eOverlap_CheckIntervals, eOverlap_CheckIntRev, eOverlap_Contained, eOverlap_Contains, eOverlap_Interval, SAnnotSelector::eOverlap_Intervals, eOverlap_Simple, eOverlap_Subset, eOverlap_SubsetRev, SAnnotSelector::eOverlap_TotalRange, eSame, CSeq_inst_Base::eTopology_circular, fBestFeat_IgnoreStrand, fCompareOverlapping, fOverlap_Default, fOverlap_IgnoreTopology, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_loc::GetId(), CBioseq_Handle::GetInst_Topology(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetLocation(), CMappedFeat::GetMappedFeature(), CMappedFeat::GetOriginalFeature(), CBioseq_Handle::GetSeqId(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CSeq_loc_Base::GetWhole(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), CSeq_loc_Base::IsPacked_pnt(), CSeq_loc_Base::IsPnt(), IsReverse(), CBioseq_Handle::IsSetInst_Topology(), CSeq_loc::IsSetStrand(), CSeq_loc_Base::IsWhole(), kInvalidSeqPos, NULL, CGetOverlappingFeaturesPlugin::postProcessDiffAmount(), CGetOverlappingFeaturesPlugin::processLoc(), CGetOverlappingFeaturesPlugin::processMainLoop(), CGetOverlappingFeaturesPlugin::processSAnnotSelector(), compile_time_bits::range(), CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), SAnnotSelector::SetFeatSubtype(), SAnnotSelector::SetFeatType(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), SAnnotSelector::SetIgnoreStrand(), SAnnotSelector::SetOverlapType(), CSeq_loc::SetPacked_int(), SAnnotSelector::SetResolveTSE(), SAnnotSelector::SetSearchUnresolved(), CSeq_loc::SetStrand(), CSeq_interval_Base::SetStrand(), CSeq_interval_Base::SetTo(), CGetOverlappingFeaturesPlugin::setUpFeatureIterator(), TestForOverlap64(), and TestForOverlapEx().

Referenced by CCdsMatchInfo::AssignOverlapMatch(), BOOST_AUTO_TEST_CASE(), CCdsToMatPeptide::ConvertInner(), GetBestCdsForMrna(), GetBestGeneForCds(), GetBestGeneForMrna(), GetBestMrnaForCds(), GetBestOverlappingFeat(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), CCleanup::IsGeneXrefUnnecessary(), CMrnaMatchInfo::OkWithoutCds(), s_GetCdsByLocation(), s_HasMobileElementForInterval(), CIntronValidator::Validate(), x_GetBestOverlapForSNP(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CCdregionValidator::x_ValidateParentPartialness(), and CRNAValidator::x_ValidateTrnaOverlap().

GetOverlappingGene()

CConstRef<CSeq_feat> GetOverlappingGene	(	const CSeq_loc &	loc,
		CScope &	scope,
		ETransSplicing	eTransSplicing = eTransSplicing_Auto
	)

Definition at line 1366 of file sequence.cpp.

References eNa_strand_both, eNa_strand_other, eOverlap_Contained, CSeqFeatData::eSubtype_gene, eTransSplicing_Auto, eTransSplicing_No, eTransSplicing_Yes, fBestFeat_IgnoreStrand, GetBestOverlappingFeat(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStrand(), and CConstRef< C, Locker >::Reset().

Referenced by AddColumnsToFeatureTable(), AdjustGene(), CRecomputeIntervals::apply(), CConvertBadCdsAndRnaToMiscFeat::apply(), ApplyFeatureSeqTableToSeqEntry(), ApplyPolicyToFeature(), CConvertCDSToPseudoGene::Convert(), CFeatureGenePanel::CreateControls(), CTruncateCDS::GetCommand(), GetGeneForFeature(), NMacroUtil::GetLocusTagFromProtRef(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), CCleanup::IsGeneXrefUnnecessary(), CCdsToMatPeptide::MergeConvert(), CHugeFileDemoApp::ProcessHugeSeqEntry(), s_CheckQuals_cdregion(), s_GetProteinName(), s_TitleFromSegment(), SetTranslExcept(), CMytestApplication::TestFeatureGeneOverlap(), CGeneOverlapProcess::TestFeatureGeneOverlap(), CHugeFileDemoApp::x_ProcessFileTraditionally(), CConvertFeatureBase::x_SimpleConversion(), and CRNAValidator::x_ValidateTrnaType().

GetOverlappingmRNA()

CConstRef<CSeq_feat> GetOverlappingmRNA	(	const CSeq_loc &	loc,
		CScope &	scope
	)

Definition at line 1572 of file sequence.cpp.

References eOverlap_Contained, CSeqFeatData::eSubtype_mRNA, and GetBestOverlappingFeat().

Referenced by AddColumnsToFeatureTable(), ApplyFeatureSeqTableToSeqEntry(), MakemRNAforCDS(), CCdsToMatPeptide::MergeConvert(), and CConvertFeatureBase::x_SimpleConversion().

GetOverlappingOperon()

CConstRef<CSeq_feat> GetOverlappingOperon	(	const CSeq_loc &	loc,
		CScope &	scope
	)

Definition at line 1600 of file sequence.cpp.

References eOverlap_Contained, CSeqFeatData::eSubtype_operon, and GetBestOverlappingFeat().

Referenced by CFeatureItem::x_AddQualOperon(), CValidError_bioseq::x_ReportGeneOverlapError(), and CGeneValidator::x_ValidateOperon().

GetOverlappingPub()

CConstRef<CSeq_feat> GetOverlappingPub	(	const CSeq_loc &	loc,
		CScope &	scope
	)

Definition at line 1586 of file sequence.cpp.

References eOverlap_Contained, CSeqFeatData::eSubtype_pub, and GetBestOverlappingFeat().

GetOverlappingSource()

CConstRef<CSeq_feat> GetOverlappingSource	(	const CSeq_loc &	loc,
		CScope &	scope
	)

Definition at line 1593 of file sequence.cpp.

References eOverlap_Contained, CSeqFeatData::eSubtype_biosrc, and GetBestOverlappingFeat().

GetParentForPart()

CBioseq_Handle GetParentForPart

(

const CBioseq_Handle &

part

)

Get the parent bioseq for a part of a segmented bioseq.

Definition at line 2688 of file sequence.cpp.

References CBioseq_set_Base::eClass_segset, and CBioseq_Handle::GetExactComplexityLevel().

Referenced by GetBioseqFromSeqLoc().

GetProteinName()

string GetProteinName

(

const CBioseq_Handle &

seq

)

Return protein name from corresponding Prot-ref feature.

Throws exception if the sequence is not a protein, or if there is no unambiguously best Prot-ref feature, or if the feature doesn't return non-empty label.

Definition at line 356 of file sequence.cpp.

References CSeqFeatData_Base::e_Prot, eGetId_Best, CBioseq_Handle::GetBioseqLength(), GetId(), CBioseq_Handle::IsProtein(), NCBI_THROW, NCBI_THROW_FMT, and compile_time_bits::range().

Referenced by CAlnVecRow::x_GetAlignmentTooltip_General().

GetPROTForProduct() [1/2]

const CSeq_feat* GetPROTForProduct	(	const CBioseq &	product,
		CScope *	scope
	)

Get the mature peptide feature of a protein.

Definition at line 2593 of file sequence.cpp.

References CScope::GetBioseqHandle().

Referenced by CValidError_bioseq::CdError(), and CDBSourceItem::x_GatherInfo().

GetPROTForProduct() [2/2]

const CSeq_feat* GetPROTForProduct

(

const CBioseq_Handle &

product

)

Definition at line 2602 of file sequence.cpp.

References CSeqFeatData_Base::e_Prot, and fi.

GetSequence()

const string& CSeqSearch::CPatternInfo::GetSequence ( void  ) const

inline

Definition at line 1182 of file sequence.hpp.

References CSeqSearch::CPatternInfo::m_Sequence.

GetSourceFeatForProduct()

CConstRef<CSeq_feat> GetSourceFeatForProduct

(

const CBioseq_Handle &

bsh

)

Definition at line 133 of file sequence.cpp.

References CSeq_loc::Assign(), eOverlap_SubsetRev, CSeqFeatData::eSubtype_biosrc, GetBestOverlappingFeat(), GetCDSForProduct(), CSeq_feat_Base::GetLocation(), CBioseq_Handle::GetScope(), CSeq_feat_Base::IsSetData(), and SeqLocRevCmpl().

Referenced by GetBioSourceForBioseq(), GetOrg_refForProduct(), GetTaxIdForProduct(), CFlatGatherer::x_CollectBioSourcesOnBioseq(), and CSourceItem::x_GatherInfo().

GetStrand()

ENa_strand CSeqSearch::CPatternInfo::GetStrand ( void  ) const

inline

Definition at line 1184 of file sequence.hpp.

References CSeqSearch::CPatternInfo::m_Strand.

GetTaxId()

TTaxId GetTaxId

(

const CBioseq_Handle &

handle

)

return the tax-id associated with a given sequence.

This will return 0 if no tax-id can be found.

Definition at line 274 of file sequence.cpp.

References GetOrg_refOrNull(), COrg_ref::GetTaxId(), and ZERO_TAX_ID.

Referenced by CLinkUtils::AddSequenceLinks(), IAlignRowHandle::GetTaxId(), CTaxTreeDS_ObjMgr::GetTaxMap(), CSeqDBTaxInfo::GetTaxNames(), CFeatGlyph::GetTooltip(), CBioSource::RemoveLineageSourceNotes(), CWindowMaskerPanel::TaxonsLoaded(), CAsn2FlatApp::x_AddSNPAnnots(), CTaxTreeToolJob::x_CreateProjectItems(), CAlignGroup::x_GetTaxId(), CWindowMaskerPanel::x_InitTaxons(), CAltValidator::x_QueryAccessions(), and CBlastTabularInfo::x_SetTaxInfo().

GetTaxIdForProduct()

TTaxId GetTaxIdForProduct

(

const CBioseq_Handle &

bsh

)

Definition at line 171 of file sequence.cpp.

References CBioseq_Handle::GetAccessSeq_id_Handle(), CBioseq_Handle::GetScope(), GetSourceFeatForProduct(), CBioseq_Handle::IsAa(), and ZERO_TAX_ID.

GetTitle() [1/2]

NCBI_XOBJUTIL_EXPORT bool GetTitle	(	const CBioseq &	seq,
		string *	title_ptr,
		TGetTitleFlags	flags = 0
	)

Definition at line 551 of file seqtitle.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Org, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeqdesc_Base::e_Source, CSeqdesc_Base::e_Title, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id::eAcc_division_mask, CSeq_id::eAcc_refseq_chromosome, CSeq_id::eAcc_refseq_mrna, CSeq_id::eAcc_refseq_ncrna, CSeq_id::eAcc_tsa, CSeq_id::eAcc_wgs, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_other_genetic, NStr::EndsWith(), NStr::eNocase, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_seg, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, fGetTitle_Organism, fGetTitle_Reconstruct, flags, fON_wgs, CMolInfo_Base::GetBiomol(), CBioseq::GetClosestDescriptor(), CSeq_id_Base::GetGeneral(), CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetRepr(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CMolInfo_Base::GetTech(), CSeq_id::IdentifyAccession(), NStr::IntToString(), CBioseq::IsAa(), CConstRef< C, Locker >::IsNull(), CBioseq_Base::IsSetInst(), CDbtag::IsSkippable(), CObject_id_Base::IsStr(), ITERATE, kEmptyStr, kMax_Int, CConstRef< C, Locker >::NotEmpty(), NPOS, NULL, prefix, s_OrganelleName(), s_TitleFromBioSource(), s_TitleFromChromosome(), rapidjson::source, NStr::StartsWith(), string, suffix, t, and CSeq_id_Base::Which().

GetTitle() [2/2]

NCBI_XOBJUTIL_EXPORT string GetTitle	(	const CBioseq_Handle &	hnd,
		TGetTitleFlags	flags = 0
	)

Definition at line 106 of file seqtitle.cpp.

References BREAK, CSeqFeatData_Base::e_Cdregion, CSeq_id_Base::e_Ddbj, CSeqdesc_Base::e_Embl, CSeq_id_Base::e_Embl, CSeqdesc_Base::e_Genbank, CSeq_id_Base::e_Genbank, CSeqFeatData_Base::e_Gene, CSeq_id_Base::e_General, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Org, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeqdesc_Base::e_Pdb, CSeq_id_Base::e_Pdb, CSeqFeatData_Base::e_Prot, CSeqdesc_Base::e_Source, CSeqdesc_Base::e_Title, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_id::eAcc_division_mask, CSeq_id::eAcc_refseq_chromosome, CSeq_id::eAcc_refseq_mrna, CSeq_id::eAcc_refseq_ncrna, CSeq_id::eAcc_tsa, CSeq_id::eAcc_wgs, CMolInfo_Base::eBiomol_cRNA, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eBiomol_ncRNA, CMolInfo_Base::eBiomol_other_genetic, CMolInfo_Base::eBiomol_pre_RNA, CMolInfo_Base::eBiomol_rRNA, CMolInfo_Base::eBiomol_scRNA, CMolInfo_Base::eBiomol_snoRNA, CMolInfo_Base::eBiomol_snRNA, CMolInfo_Base::eBiomol_tmRNA, CMolInfo_Base::eBiomol_transcribed_RNA, CMolInfo_Base::eBiomol_tRNA, CSeq_inst_Base::eMol_aa, NStr::EndsWith(), NStr::eNocase, NStr::EqualNocase(), CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_seg, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, fFGL_Content, CSeqMap::fFindGap, fGetTitle_NoExpensive, fGetTitle_Organism, fGetTitle_Reconstruct, flags, fON_wgs, CMolInfo_Base::GetBiomol(), CBioseq_Handle::GetBioseqMolType(), CSeq_entry_Handle::GetCompleteSeq_entry(), CPDB_block_Base::GetCompound(), CSeq_id_Base::GetGeneral(), CBioseq_Handle::GetId(), CBioseq_Handle::GetInst_Repr(), GetLabel(), CSeqdesc_Base::GetOrg(), CSeqdesc_Base::GetPdb(), CBioseq_Handle::GetScope(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CMolInfo_Base::GetTech(), CSeqdesc_Base::GetTitle(), CBioseq_Handle::GetTopLevelEntry(), CSeq_id::IdentifyAccession(), NStr::IntToString(), CConstRef< C, Locker >::IsNull(), isprint(), CDbtag::IsSkippable(), CObject_id_Base::IsStr(), ITERATE, kEmptyStr, CConstRef< C, Locker >::NotEmpty(), NPOS, NULL, prefix, NStr::Replace(), CConstRef< C, Locker >::Reset(), s_FlyCG_PtoR(), s_OrganelleName(), s_TitleFromBioSource(), s_TitleFromChromosome(), s_TitleFromProtein(), s_TitleFromSegment(), rapidjson::source, NStr::StartsWith(), string, suffix, t, and CSeq_id_Base::Which().

Referenced by PT::CWorkspace::BeginLabelEdit(), CEditingBtnsPanel::CEditingBtnsPanel(), CFeedbackWizard::Create(), CSubjectMap_Factory_Base::extractSeqVector(), ExtractSeqVector(), CWinMaskUtil::CIdSet_TextMatch::find(), CPub::GetTitles(), and CTitleProcess::SeqEntryProcess().

GetWidth()

TSeqPos CFastaOstream::GetWidth ( void  ) const

inline

Other parameters...

Definition at line 855 of file sequence.hpp.

IsPseudo()

bool IsPseudo	(	const CSeq_feat &	feat,
		CScope &	scope
	)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to see if a feature is pseudo.

Looks for pseudo flag set on feature, looks for pseudogene qualifier on feature, performs same checks for gene associated with feature

Parameters

feat	Seq-feat to check
scope	CScope to use when looking for associated gene

Returns

Boolean return value indicates whether any of the "pseudo" markers are found

Definition at line 1428 of file sequence.cpp.

References NStr::EqualNocase(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), GetGeneForFeature(), CGene_ref_Base::GetPseudo(), CSeq_feat_Base::GetPseudo(), CSeq_feat_Base::GetQual(), CSeq_feat_Base::GetXref(), CSeqFeatData_Base::IsGene(), CGene_ref_Base::IsSetPseudo(), CSeq_feat_Base::IsSetPseudo(), CSeq_feat_Base::IsSetQual(), CSeq_feat_Base::IsSetXref(), and ITERATE.

Referenced by CGenericPropsPanel::CreateControls(), DoesFeatureHaveUnnecessaryException(), CCleanup::ExtendToStopIfShortAndNotPartial(), g_InstantiateMissingProteins(), CRetranslateCDS::GetCommand(), CCDSTranslationProblems::GetNonsenseIntrons(), CCleanup::RemovePseudoProduct(), s_HasUnprocessedCdregions(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CImpFeatValidator::Validate(), CValidError_bioseqset::ValidateGenProdSet(), CValidError_imp::ValidateSeqLoc(), CCleanup::WGSCleanup(), CCleanup::x_AddLowQualityException(), CCleanupApp::x_BatchExtendCDS(), CCDSTranslationProblems::x_CountNonsenseIntrons(), CImportFeatTable::x_DoImportCDS(), CCDSTranslationPanel::x_IsPseudo(), CMacroFunction_EditFeatLocation::x_RetranslateCDS(), CValidError_bioseq::x_TranscriptIDsMatch(), CFeatTableEdit::xGenerate_mRNA_Product(), and CFeatureTableReader::xMoveCdRegions().

NCBI_EXCEPTION_DEFAULT()

CSeqIdFromHandleException::NCBI_EXCEPTION_DEFAULT	(	CSeqIdFromHandleException	,
		CException
	)

OnPatternFound()

virtual bool CSeqSearch::IClient::OnPatternFound ( const TPatternInfo &  pat_info, TSeqPos  pos  )

pure virtual

Referenced by CSeqSearch::Search().

operator*()

const SCurrentGapInfo& CBioseqGaps_CI::operator* ( void  ) const

inline

Get information about the gap we're currently on.

Definition at line 1654 of file sequence.hpp.

References CBioseqGaps_CI::x_GetCurrent().

operator++()

CBioseqGaps_CI& CBioseqGaps_CI::operator++ ( void  )

inline

Move the iterator forward to next gap (or the end, if there are no more to return)

Definition at line 1617 of file sequence.hpp.

References CBioseqGaps_CI::x_Next().

operator->()

const SCurrentGapInfo* CBioseqGaps_CI::operator-> ( void  ) const

inline

Get information about the gap we're currently on.

Definition at line 1659 of file sequence.hpp.

References CBioseqGaps_CI::x_GetCurrent().

operator=()

CDeflineGenerator& CDeflineGenerator::operator= ( const CDeflineGenerator &  )

private

Params()

CBioseqGaps_CI::Params::Params ( void  )

inline

Default ctor gives params which are usually reasonable.

Definition at line 1579 of file sequence.hpp.

postProcessDiffAmount()

virtual void CGetOverlappingFeaturesPlugin::postProcessDiffAmount ( Int8 &  cur_diff, CRef< CSeq_loc > &  cleaned_loc_this_iteration, CRef< CSeq_loc > &  candidate_feat_loc, CScope &  scope, SAnnotSelector &  sel, TSeqPos  circular_length  )

pure virtual

Implemented in CCdsForMrnaPlugin.

Referenced by GetOverlappingFeatures(), and CCdsForMrnaPlugin::postProcessDiffAmount().

processLoc()

virtual void CGetOverlappingFeaturesPlugin::processLoc ( CBioseq_Handle &  bioseq_handle, CRef< CSeq_loc > &  loc, TSeqPos  circular_length  )

pure virtual

Implemented in CCdsForMrnaPlugin.

Referenced by GetOverlappingFeatures(), and CCdsForMrnaPlugin::processLoc().

processMainLoop()

virtual void CGetOverlappingFeaturesPlugin::processMainLoop ( bool &  shouldContinueToNextIteration, CRef< CSeq_loc > &  cleaned_loc_this_iteration, CRef< CSeq_loc > &  candidate_feat_loc, EOverlapType &  overlap_type_this_iteration, bool &  revert_locations_this_iteration, CBioseq_Handle &  bioseq_handle, const CMappedFeat &  feat, TSeqPos  circular_length, SAnnotSelector::EOverlapType  annot_overlap_type  )

pure virtual

Implemented in CCdsForMrnaPlugin.

Referenced by GetOverlappingFeatures(), and CCdsForMrnaPlugin::processMainLoop().

processSAnnotSelector()

virtual void CGetOverlappingFeaturesPlugin::processSAnnotSelector ( SAnnotSelector &  sel )

pure virtual

Implemented in CCdsForMrnaPlugin.

Referenced by GetOverlappingFeatures(), and CCdsForMrnaPlugin::processSAnnotSelector().

ProductToSource()

CRef<CSeq_loc> ProductToSource	(	const CSeq_feat &	feat,
		const CSeq_loc &	prod_loc,
		TP2SFlags	flags = 0,
		CScope *	scope = 0
	)

Definition at line 841 of file sequence.cpp.

References _ASSERT, flags, fP2S_Extend, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), GetLength(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::IsCdregion(), IsReverse(), SRelLoc::m_ParentLoc, SRelLoc::m_Ranges, max(), NON_CONST_ITERATE, CConstRef< C, Locker >::Reset(), and SRelLoc::Resolve().

Referenced by CCdregionValidator::MapToNTCoords().

ResetFlag()

void CFastaOstream::ResetFlag ( EFlags  flag )

inline

Definition at line 860 of file sequence.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CBlastDBExtractor::ExtractFasta(), and CBlastDB_FastaFormatter::Write().

Resolve() [1/2]

CRef< CSeq_loc > SRelLoc::Resolve	(	const CSeq_loc &	new_parent,
		CScope *	scope = 0,
		SRelLoc::TFlags	flags = 0
	)		const

Definition at line 4583 of file sequence.cpp.

References _ASSERT, delta(), CInt_fuzz::eAmplify, eNa_strand_unknown, CSerialObject::Equals(), ERR_POST_X, f(), first(), CSeq_loc_mix_Base::Get(), CSeq_loc::GetLabel(), GetLength(), CConstRef< C, Locker >::GetPointer(), IsReverse(), ITERATE, label, SRelLoc::m_Ranges, CConstRef< C, Locker >::Reset(), result, Reverse(), CSeq_loc_mix_Base::Set(), CSeq_interval_Base::SetFrom(), CSeq_point_Base::SetFuzz(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CSeq_interval_Base::SetId(), CSeq_point_Base::SetId(), CSeq_loc::SetInt(), CSeq_loc::SetPnt(), CSeq_point_Base::SetPoint(), CSeq_interval_Base::SetStrand(), CSeq_point_Base::SetStrand(), CSeq_interval_Base::SetTo(), and Warning().

Resolve() [2/2]

CRef<CSeq_loc> SRelLoc::Resolve ( CScope *  scope = 0, TFlags  flags = 0  ) const

inline

Definition at line 1143 of file sequence.hpp.

References flags, and SRelLoc::m_ParentLoc.

Referenced by ProductToSource(), CSeqUtils::RemapChildToParent(), s_RemapChildToParent(), and SourceToProduct().

ReverseComplement()

void ReverseComplement	(	CSeq_inst &	seq,
		CScope *	scope
	)

Reverse complement a Bioseq in place.

If delta sequence, will also need to reverse order of segments

Definition at line 5142 of file sequence.cpp.

References CDelta_seq_Base::e_Literal, CDelta_seq_Base::e_Loc, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CSeq_inst_Base::GetExt(), CSeq_inst_Base::GetLength(), CSeq_literal_Base::GetLength(), CSeq_inst_Base::GetRepr(), CSeq_literal_Base::GetSeq_data(), CSeq_ext_Base::IsDelta(), CSeq_data_Base::IsGap(), CSeq_inst_Base::IsSetExt(), NCBI_THROW, NON_CONST_ITERATE, CSeqportUtil::ReverseComplement(), SeqLocRevCmpl(), CSeq_inst_Base::SetExt(), CSeq_inst_Base::SetSeq_data(), and CSeq_literal_Base::SetSeq_data().

SAmbigCount()

CSequenceAmbigTrimmer::SAmbigCount::SAmbigCount ( const TSignedSeqPos  iTrimDirection )

inline

Definition at line 1470 of file sequence.hpp.

SCurrentGapInfo()

CBioseqGaps_CI::SCurrentGapInfo::SCurrentGapInfo ( void  )

inline

Constructor initializes to state that it should be when the iterator first starts.

Definition at line 1629 of file sequence.hpp.

Search() [1/2]

void CSeqSearch::Search

(

const CBioseq_Handle &

seq

)

Search the sequence for patterns.

See also

AddNucleotidePattern

Definition at line 4940 of file sequence.cpp.

References CBioseq_Handle::eCoding_Iupac, CSeq_inst_Base::eTopology_circular, CBioseq_Handle::GetInst_Topology(), CBioseq_Handle::GetSeqVector(), i, CSeqSearch::m_Client, CSeqSearch::m_Fsa, CSeqSearch::m_LongestPattern, NULL, and CSeqVector::size().

Search() [2/2]

int CSeqSearch::Search	(	int	current_state,
		char	ch,
		int	position,
		int	length = kMax_Int
	)

Low level search method.

The user is responsible for feeding each character in turn, keep track of the position in the text and provide the length in case of a circular topoloy.

Definition at line 4903 of file sequence.cpp.

References int, ITERATE, CSeqSearch::m_Client, CSeqSearch::m_Fsa, NULL, and CSeqSearch::IClient::OnPatternFound().

SetAllFlags()

void CFastaOstream::SetAllFlags ( TFlags  flags )

inline

Definition at line 858 of file sequence.hpp.

References flags.

Referenced by CBlastDB_FastaFormatter::CBlastDB_FastaFormatter(), CVdbFastaExtractor::DumpAll(), CBlastDB_FastaFormatter::DumpAll(), CSeqFormatter::DumpAll(), CBlastDBExtractor::ExtractFasta(), CFastaProcess::SeqEntryProcess(), CVdbFastaExtractor::Write(), and CFastaOstreamComp::x_GetFastaOstream().

SetClient()

void CSeqSearch::SetClient ( IClient *  client )

inline

Definition at line 1251 of file sequence.hpp.

References client, and CSeqSearch::m_Client.

SetFlag()

void CFastaOstream::SetFlag ( EFlags  flag )

inline

Definition at line 859 of file sequence.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CBlastDBExtractor::ExtractFasta(), GetSequenceStringFromLoc(), CFastaExportJob::Run(), CFastaProcess::SeqEntryProcess(), CFastaTextDisplay::Update(), CBlastDB_FastaFormatter::Write(), and CFastaTitleItem::x_GetTitle().

SetGapMode()

void CFastaOstream::SetGapMode ( EGapMode  mode )

inline

Definition at line 861 of file sequence.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CFastaProcess::SeqEntryProcess().

SetMask()

void CFastaOstream::SetMask	(	EMaskType	type,
		CConstRef< CSeq_loc >	location
	)

Definition at line 3450 of file sequence.cpp.

References CFastaOstream::eSoftMask, location, CFastaOstream::m_HardMask, and CFastaOstream::m_SoftMask.

Referenced by BOOST_AUTO_TEST_CASE(), CBlastDBExtractor::ExtractFasta(), and CBlastDB_FastaFormatter::Write().

setUpFeatureIterator()

virtual void CGetOverlappingFeaturesPlugin::setUpFeatureIterator ( CBioseq_Handle &  bioseq_handle, unique_ptr< CFeat_CI > &  feat_ci, TSeqPos  circular_length, CRange< TSeqPos > &  range, const CSeq_loc &  loc, SAnnotSelector &  sel, CScope &  scope, ENa_strand &  strand  )

pure virtual

Implemented in CCdsForMrnaPlugin.

Referenced by GetOverlappingFeatures(), and CCdsForMrnaPlugin::setUpFeatureIterator().

SetWidth()

void CFastaOstream::SetWidth

(

TSeqPos

width

)

Definition at line 3456 of file sequence.cpp.

References AutoPtr< X, Del >::get(), CFastaOstream::m_Dashes, CFastaOstream::m_LC_Ns, CFastaOstream::m_LC_Xs, CFastaOstream::m_UC_Ns, CFastaOstream::m_UC_Xs, CFastaOstream::m_Width, and AutoPtr< X, Del >::reset().

Referenced by CBlastDB_FastaFormatter::CBlastDB_FastaFormatter(), CVdbFastaExtractor::DumpAll(), CSeqFormatter::DumpAll(), CBlastDBExtractor::ExtractFasta(), s_CheckIdLookup(), and CVdbFastaExtractor::Write().

SkipBioseq() [1/2]

virtual bool CFastaOstream::SkipBioseq ( const CBioseq &  )

inlinevirtual

Used only by Write(CSeq_entry[_Handle], ...); permissive by default.

Definition at line 837 of file sequence.hpp.

Referenced by CFastaOstream::Write().

SkipBioseq() [2/2]

virtual bool CFastaOstream::SkipBioseq ( const CBioseq_Handle &  handle )

inlinevirtual

Delegates to the non-handle version by default for compatibility with older code; newer code should override this version.

Definition at line 841 of file sequence.hpp.

References CBioseq_Handle::GetCompleteBioseq().

SourceToProduct()

CRef<CSeq_loc> SourceToProduct	(	const CSeq_feat &	feat,
		const CSeq_loc &	source_loc,
		TS2PFlags	flags = 0,
		CScope *	scope = 0,
		int *	frame = 0
	)

Definition at line 790 of file sequence.cpp.

References _ASSERT, ERR_POST_X, flags, SRelLoc::fNoMerge, fS2P_AllowTer, fS2P_NoMerge, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), GetLength(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::IsCdregion(), IsReverse(), SRelLoc::m_ParentLoc, SRelLoc::m_Ranges, max(), NON_CONST_ITERATE, CConstRef< C, Locker >::Reset(), SRelLoc::Resolve(), and Warning().

Referenced by TestOneCDS(), and CCdregionValidator::x_ValidateCodebreak().

SRelLoc() [1/2]

SRelLoc::SRelLoc	(	const CSeq_loc &	parent,
		const CSeq_loc &	child,
		CScope *	scope = 0,
		SRelLoc::TFlags	flags = 0
	)

Beware: treats locations corresponding to different sequences as disjoint, even if one is actually a segment of the other.

:-/

Definition at line 4421 of file sequence.cpp.

References delta(), CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, eNa_strand_unknown, f(), flags, SRelLoc::fNoMerge, GetLength(), IsReverse(), IsSameBioseq(), SRelLoc::m_Ranges, CInt_fuzz::Negative(), CConstRef< C, Locker >::Reset(), Reverse(), and SameOrientation().

SRelLoc() [2/2]

SRelLoc::SRelLoc ( const CSeq_loc &  parent, const TRanges &  ranges  )

inline

For manual work. As noted above, ranges need not contain any IDs.

Definition at line 1140 of file sequence.hpp.

Translate() [1/7]

void CSeqTranslator::Translate ( const CSeq_feat &  cds, CScope &  scope, string &  prot, bool  include_stop = true, bool  remove_trailing_X = false, bool *  alt_start = 0  )

static

Translate a CDRegion into a protein.

Definition at line 4183 of file sequence.cpp.

References CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eOffset_FromStart, CCode_break_Base::GetAa(), CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode(), CCdregion_Base::GetCode_break(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CCode_break_Base::GetLoc(), CSeq_feat_Base::GetLocation(), CCode_break_Base::C_Aa::GetNcbieaa(), i, CSeqFeatData_Base::IsCdregion(), CCode_break_Base::C_Aa::IsNcbieaa(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CCdregion_Base::IsSetCode(), CCdregion_Base::IsSetCode_break(), CCdregion_Base::IsSetFrame(), ITERATE, LocationOffset(), NULL, prot, and x_Translate().

Translate() [2/7]

void CSeqTranslator::Translate ( const CSeq_loc &  loc, const CBioseq_Handle &  handle, string &  prot, const CGenetic_code *  code = NULL, bool  include_stop = true, bool  remove_trailing_X = false, bool *  alt_start = 0  )

static

utility function: translate a given location on a sequence

Definition at line 4150 of file sequence.cpp.

References CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CBioseq_Handle::GetScope(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), prot, and x_Translate().

Translate() [3/7]

void CSeqTranslator::Translate ( const CSeq_loc &  loc, CScope &  scope, string &  prot, const CGenetic_code *  code = NULL, bool  include_stop = true, bool  remove_trailing_X = false, bool *  alt_start = 0  )

static

utility function: translate a given location on a sequence

Definition at line 4167 of file sequence.cpp.

References CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), prot, and x_Translate().

Translate() [4/7]

void CSeqTranslator::Translate ( const CSeqVector &  seq, string &  prot, const CGenetic_code *  code, bool  include_stop = true, bool  remove_trailing_X = false, bool *  alt_start = NULL, bool  is_5prime_complete = true, bool  is_3prime_complete = true  )

static

Translate a seq-vector using a specified genetic code if the code is NULL, then the default genetic code is used.

Parameters

seq	CSeqVector of sequence to be translated
code	Genetic code to use for translation (NULL to use default)
include_stop	If true, translate through stop codons and include trailing stop (true by default)
remove_trailing_X	If true, remove trailing Xs from protein translation (false by default)
alt_start	Pointer to bool to indicate whether an alternative start codon was used
is_5prime_complete	If true, only translate first codon if start codon, otherwise translate as dash (-) to indicate problem with sequence

Definition at line 4123 of file sequence.cpp.

References prot, and x_Translate().

Translate() [5/7]

void CSeqTranslator::Translate ( const CSeqVector &  seq, string &  prot, TTranslationFlags  flags = fDefault, const CGenetic_code *  code = NULL, bool *  alt_start = NULL  )

static

Translate a seq-vector using a specified genetic code if the code is NULL, then the default genetic code is used.

Parameters

seq	CSeqVector of sequence to be translated
code	Genetic code to use for translation (NULL to use default)
flags	Binary OR of "ETranslationFlags"
alt_start	Pointer to bool to indicate whether an alternative start codon was used

Definition at line 4136 of file sequence.cpp.

References flags, prot, and x_Translate().

Translate() [6/7]

void CSeqTranslator::Translate ( const string &  seq, string &  prot, const CGenetic_code *  code, bool  include_stop = true, bool  remove_trailing_X = false, bool *  alt_start = NULL, bool  is_5prime_complete = true, bool  is_3prime_complete = true  )

static

Translate a string using a specified genetic code.

Parameters

seq	String containing IUPAC representation of sequence to be translated
code	Genetic code to use for translation (NULL to use default)
include_stop	If true, translate through stop codons and include trailing stop (true by default)
remove_trailing_X	If true, remove trailing Xs from protein translation (false by default)
alt_start	Pointer to bool to indicate whether an alternative start codon was used
is_5prime_complete	If true, only translate first codon if start codon, otherwise translate as dash (-) to indicate problem with sequence

Definition at line 4095 of file sequence.cpp.

References prot, and x_Translate().

Referenced by CCDSTranslationPanel::AdjustForStopCodonHyperlinkClicked(), CFeatGapInfo::AdjustProteinSeq(), AdjustSingleFeature(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CConvertCdsToMiscFeat::DetectStartStopCodons(), DoesCodingRegionEndWithStopCodon(), CCleanup::ExtendToStopIfShortAndNotPartial(), CSeqTranslator::FindBestFrame(), CScore_CdsInternalStops::Get(), GetRetranslateCDSCommand(), CLocationEditPolicy::Interpret3Policy(), CLocationEditPolicy::Interpret5Policy(), CMakeCdrProds::MakeCdrProds(), variation_ref::CVariationUtil::PrecursorToProt(), CTabularFormatter_StopCodonChanges::Print(), CGlimmerReader::Read(), CRetranslateCDS::RetranslateCDSCommand(), CAddGlobalCodeBreak::RetranslateCDSCommand(), CExtendCDSToStop::RetranslateCDSCommand(), CTestSingleAln_All::RunTest(), s_CompareProtProdToTrans(), ApplyCDSFrame::s_FindMatchingFrame(), CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame(), s_GetCdsSequence(), s_GetGermlineTranslation(), CCmdCreateCDS::s_GetProductSequence(), variation_ref::CVariationUtil::s_UntranslateProt(), variation::CVariationUtil::s_UntranslateProt(), CIgBlastTabularInfo::SetAirrFormatData(), SetCdrFwrSeq(), CCleanup::SetCDSPartialsByFrameAndTranslation(), CIgBlastTabularInfo::SetIgAnnotation(), CIgBlastTabularInfo::SetIgCDR3FWR4Annotation(), CValidError_bioseq::SuppressTrailingXMsg(), TestTrimForFrame(), variation::Translate(), Translate(), CCdregion_translate::TranslateCdregion(), CPaintSequence::TranslateCDS(), TranslateCodingRegionForValidation(), TruncateCDSAtStop(), CTruncateCDS::TruncateProteinFeat(), CPaintSequence::UpdateData(), CFeatureItem::x_AddQualTranslation(), CDisplaySeqalign::x_AddTranslationForLocalSeq(), CCleanupApp::x_BatchExtendCDS(), CFeaturePropagator::x_CdsCleanupPartials(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CImportFeatTable::x_DoImportCDS(), CAdjustFeaturesForGaps::x_DoOne(), COrfSearchJob::x_DoSearch(), CCdsGlyph::x_Draw(), CAlignGlyph::x_DrawAlignRowSequence(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), CAlignGlyph::x_DrawUnalignedRowSequence(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CCDSTranslationProblems::x_GetTranslExceptProblems(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CReportTrim::x_RetranslateCDS(), variation::CHgvsParser::x_SeqLiteralToStr(), CCDSTranslationPanel::x_Translate(), and CCdregionValidator::x_ValidateConflict().

Translate() [7/7]

void CSeqTranslator::Translate ( const string &  seq, string &  prot, TTranslationFlags  flags = fDefault, const CGenetic_code *  code = NULL, bool *  alt_start = NULL  )

static

Translate a string using a specified genetic code.

Parameters

seq	String containing IUPAC representation of sequence to be translated
code	Genetic code to use for translation (NULL to use default)
flags	Binary OR of "ETranslationFlags"
alt_start	Pointer to bool to indicate whether an alternative start codon was used

Definition at line 4108 of file sequence.cpp.

References flags, prot, and x_Translate().

TranslateCdregion() [1/2]

void CCdregion_translate::TranslateCdregion ( string &  prot, const CBioseq_Handle &  bsh, const CSeq_loc &  loc, const CCdregion &  cdr, bool  include_stop = true, bool  remove_trailing_X = false, bool *  alt_start = 0, ETranslationLengthProblemOptions  options = eThrowException  )

static

translation coding region into ncbieaa protein sequence

Definition at line 4384 of file sequence.cpp.

References CBioseq_Handle::GetScope(), prot, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and CSeqTranslator::Translate().

Referenced by CPromote::x_PromoteCdregion().

TranslateCdregion() [2/2]

void CCdregion_translate::TranslateCdregion ( string &  prot, const CSeq_feat &  cds, CScope &  scope, bool  include_stop = true, bool  remove_trailing_X = false, bool *  alt_start = 0, ETranslationLengthProblemOptions  options = eThrowException  )

static

Definition at line 4401 of file sequence.cpp.

References _ASSERT, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), CBioseq_Handle::GetScope(), CSeqFeatData_Base::IsCdregion(), prot, and CSeqTranslator::Translate().

TranslateToProtein()

CRef< CBioseq > CSeqTranslator::TranslateToProtein ( const CSeq_feat &  cds, CScope &  scope  )

static

Definition at line 3839 of file sequence.cpp.

References AddAAToDeltaSeq(), AddGapToDeltaSeq(), CSeqVector::begin(), CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, CSeq_inst_Base::eMol_aa, NStr::EndsWith(), eOffset_FromStart, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CSeqMap::eSeqGap, NStr::Find(), CCode_break_Base::GetAa(), CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode(), CCdregion_Base::GetCode_break(), CTrans_table::GetCodonResidue(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CCode_break_Base::GetLoc(), CSeq_feat_Base::GetLocation(), CCode_break_Base::C_Aa::GetNcbieaa(), CSeqVector::GetSeqMap(), CTrans_table::GetStartResidue(), CGen_code_table::GetTransTable(), CSeqMap_CI::GetType(), CSeqVector_CI::HasZeroGapBefore(), i, CSeqFeatData_Base::IsCdregion(), CSeqVector::IsInGap(), CCode_break_Base::C_Aa::IsNcbieaa(), CSeq_loc::IsPartialStart(), CCdregion_Base::IsSetCode(), CCdregion_Base::IsSetCode_break(), CCdregion_Base::IsSetFrame(), CSeqMap_CI::IsUnknownLength(), ITERATE, LocationOffset(), mod(), CTrans_table::NextCodonState(), NON_CONST_ITERATE, NULL, offset, prot, and CSeqVector::size().

Referenced by CCleanup::AddProtein(), BOOST_AUTO_TEST_CASE(), CCmdAddCDS::Execute(), GetRetranslateCDSCommand(), CCdsToMatPeptide::MergeConvert(), RetranslateCDS(), RetranslateCdsForNucProtSet(), SetNewProteinSequence(), TestOneGapSeq(), TranslateCDSCommand(), TruncateCDSAtStop(), CFeaturePropagator::x_CdsStopAtStopCodon(), CVectorTrimPanel::x_RetranslateCDS(), CFastaOstreamEx::x_WriteTranslatedCds(), CFeatTableEdit::xGenerate_mRNA_Product(), and CFeatureTableReader::xTranslateProtein().

UsePDBCompoundForDefline()

bool CDeflineGenerator::UsePDBCompoundForDefline ( void  ) const

inline

Definition at line 145 of file create_defline.hpp.

Write() [1/4]

void CFastaOstream::Write	(	const CBioseq &	seq,
		const CSeq_loc *	location = 0,
		bool	no_scope = false,
		const string &	custom_title = kEmptyStr
	)

Definition at line 3389 of file sequence.cpp.

References CScope::AddBioseq(), CDelta_seq_Base::e_Loc, CSeq_data_Base::e_Ncbieaa, CBioseq_Handle::eCoding_Iupac, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CBioseq_Base::GetInst(), CObjectManager::GetInstance(), CSeq_inst_Base::GetRepr(), CSeqVector::IsProtein(), ITERATE, location, NULL, CSeqVector::SetCoding(), CFastaOstream::Write(), CFastaOstream::x_GetMaskingStates(), CFastaOstream::x_WriteSeqIds(), CFastaOstream::x_WriteSeqTitle(), and CFastaOstream::x_WriteSequence().

Write() [2/4]

void CFastaOstream::Write ( const CBioseq_Handle &  handle, const CSeq_loc *  location = 0, const string &  custom_title = kEmptyStr  )

virtual

Definition at line 2748 of file sequence.cpp.

References location, CFastaOstream::WriteSequence(), and CFastaOstream::WriteTitle().

Write() [3/4]

void CFastaOstream::Write	(	const CSeq_entry &	entry,
		const CSeq_loc *	location = 0,
		bool	no_scope = false
	)

These versions may set up a temporary object manager scope In the common case of a raw bioseq, no scope is needed.

Definition at line 3365 of file sequence.cpp.

References CScope::AddTopLevelSeqEntry(), CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CObjectManager::GetInstance(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), ITERATE, location, CSeq_entry_Base::Which(), and CFastaOstream::Write().

Write() [4/4]

void CFastaOstream::Write ( const CSeq_entry_Handle &  handle, const CSeq_loc *  location = 0  )

virtual

Unspecified locations designate complete sequences; non-empty custom titles override the usual title determination logic.

Definition at line 2727 of file sequence.cpp.

References eOverlap_Interval, CSeq_entry_Handle::GetScope(), kInvalidSeqPos, location, CSeq_loc::SetWhole(), CFastaOstream::SkipBioseq(), and TestForOverlap().

Referenced by BOOST_AUTO_TEST_CASE(), CMytestApplication::DoProcessStreamFasta(), CReadBlastApp::dump_fasta_for_pretty_blast(), CVdbFastaExtractor::DumpAll(), CSeqFormatter::DumpAll(), CBlastDBExtractor::ExtractFasta(), CAsn2FastaApp::HandleSeqEntry(), CFastaExportJob::Run(), s_CheckIdLookup(), CFastaProcess::SeqEntryProcess(), CFastaTextDisplay::Update(), CSortedProteins::View(), CFastaOstream::Write(), CVdbFastaExtractor::Write(), CBlastDB_FastaFormatter::Write(), CBLASTSeqToolJob::x_CreateProjectItems(), CWindowMaskerJob::x_CreateProjectItems(), and CFastaOstreamComp::x_Write().

WriteAllModsAsFasta()

void CFastaOstream::SGapModText::WriteAllModsAsFasta

(

CNcbiOstream &

out

)

const

This will write the modifiers in FASTA format.

(example: "[gap-type=short_arm]")

Definition at line 3467 of file sequence.cpp.

References CFastaOstream::SGapModText::gap_linkage_evidences, CFastaOstream::SGapModText::gap_type, NStr::Join(), and out().

Referenced by CFastaOstream::x_WriteSequence().

WriteSequence()

void CFastaOstream::WriteSequence ( const CBioseq_Handle &  handle, const CSeq_loc *  location = 0, CSeq_loc::EOpFlags  merge_flags = CSeq_loc::fMerge_AbuttingOnly  )

virtual

Definition at line 3322 of file sequence.cpp.

References CSeqMap::CanResolveRange(), CSeq_data_Base::e_Ncbieaa, CBioseq_Handle::eCoding_Iupac, eSeqLocCheck_error, CFastaOstream::fAssembleParts, CSeqMap::fFindInnerRef, CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqId(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetSeqVector(), CBioseq_Handle::GetTSE_Handle(), CSeqVector::IsProtein(), CBioseq_Handle::IsSetInst_Seq_data(), label, location, CFastaOstream::m_Flags, CFastaOstream::m_HardMask, CFastaOstream::m_SoftMask, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), Seq_loc_Merge(), SeqLocCheck(), CSeqVector::SetCoding(), SSeqMapSelector::SetLinkUsedTSE(), CFastaOstream::x_GetMaskingStates(), and CFastaOstream::x_WriteSequence().

Referenced by CSeqFormatter::DumpAll(), CBlastDBExtractor::ExtractFasta(), GetSequenceStringFromLoc(), CFastaOstream::Write(), CBlastDB_FastaFormatter::Write(), CFastaOstreamEx::WriteFeature(), and CFastaOstreamEx::x_WriteTranslatedCds().

WriteTitle() [1/2]

void CFastaOstream::WriteTitle	(	const CBioseq &	seq,
		const CSeq_loc *	location = 0,
		bool	no_scope = false,
		const string &	custom_title = kEmptyStr
	)

Definition at line 3022 of file sequence.cpp.

WriteTitle() [2/2]

void CFastaOstream::WriteTitle ( const CBioseq_Handle &  handle, const CSeq_loc *  location = 0, const string &  custom_title = kEmptyStr  )

virtual

Definition at line 3033 of file sequence.cpp.

Referenced by CMytestApplication::DoProcessStreamDefline(), CAsn2FastaApp::HandleSeqEntry(), CFastaOstream::Write(), and CFastaTitleItem::x_GetTitle().

x_AddNucleotidePattern()

void CSeqSearch::x_AddNucleotidePattern ( const string &  name, string &  pattern, Int2  cut_site, ENa_strand  strand, TSearchFlags  flags  )

private

Definition at line 5064 of file sequence.cpp.

References buffer, flags, kEmptyStr, CSeqSearch::m_LongestPattern, CSeqSearch::CPatternInfo::m_Sequence, CSeqSearch::CPatternInfo::m_Strand, CSeqSearch::x_AddPattern(), CSeqSearch::x_ExpandPattern(), and CSeqSearch::x_IsExpandPattern().

Referenced by CSeqSearch::AddNucleotidePattern().

x_AddPattern()

void CSeqSearch::x_AddPattern ( TPatternInfo &  pat_info, string &  sequence, TSearchFlags  flags  )

private

Definition at line 5116 of file sequence.cpp.

References flags, NON_CONST_ITERATE, swap(), CSeqSearch::x_IsAllowMismatch(), and CSeqSearch::x_StorePattern().

Referenced by CSeqSearch::x_AddNucleotidePattern(), and CSeqSearch::x_ExpandPattern().

x_AdjustProteinTitleSuffix()

void CDeflineGenerator::x_AdjustProteinTitleSuffix ( const CBioseq_Handle &  bsh )

private

Definition at line 3248 of file create_defline.cpp.

References CTempString::empty(), CConstRef< C, Locker >::Empty(), NStr::EndsWith(), NStr::eNocase, NStr::EqualNocase(), NStr::eReverseSearch, CTempString::find(), NStr::Find(), COrgName_Base::C_Name::GetBinomial(), CBioseqIndex::GetBioseqForProduct(), CSeqEntryIndex::GetBioseqIndex(), CBioSource_Base::GetGenome(), CBinomialOrgName_Base::GetGenus(), COrgName_Base::GetName(), CBioSource::GetOrgname(), CBinomialOrgName_Base::GetSpecies(), CBioSource::GetTaxname(), int, COrgName_Base::C_Name::IsBinomial(), CBioSource_Base::IsSetGenome(), CBinomialOrgName_Base::IsSetGenus(), COrgName_Base::IsSetName(), CBioSource::IsSetOrgname(), CBinomialOrgName_Base::IsSetSpecies(), CBioSource::IsSetTaxname(), CTempString::length(), CWeakRef< C, Locker >::Lock(), CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_Taxname, NCBI_GENOME, CConstRef< C, Locker >::NotEmpty(), NPOS, s_proteinOrganellePrefix, s_TitleEndsInOrganism(), s_TrimMainTitle(), str(), string, x_GetSourceFeatViaCDS(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

x_AdjustProteinTitleSuffixIdx()

void CDeflineGenerator::x_AdjustProteinTitleSuffixIdx ( const CBioseq_Handle &  bsh )

private

Definition at line 3098 of file create_defline.cpp.

References CTempString::empty(), CConstRef< C, Locker >::Empty(), NStr::EndsWith(), NStr::eNocase, NStr::EqualNocase(), NStr::eReverseSearch, CTempString::find(), NStr::Find(), CBioseqIndex::GetBioseqForProduct(), CSeqEntryIndex::GetBioseqIndex(), CBioseqIndex::GetBioSource(), CBioseqIndex::GetDescTaxname(), CBioseqIndex::GetGenome(), CBioseqIndex::GetGenus(), CBioseqIndex::GetOrganelle(), CBioseqIndex::GetSpecies(), CBioseqIndex::GetTaxname(), CBioSource::GetTaxname(), int, CBioSource::IsSetTaxname(), CTempString::length(), CWeakRef< C, Locker >::Lock(), CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_Taxname, NCBI_GENOME, CConstRef< C, Locker >::NotEmpty(), NPOS, s_proteinOrganellePrefix, s_TitleEndsInOrganism(), s_TrimMainTitle(), str(), string, x_GetSourceFeatViaCDS(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

x_CDShasLowQualityException()

bool CDeflineGenerator::x_CDShasLowQualityException ( const CSeq_feat &  sft )

private

Definition at line 2102 of file create_defline.cpp.

References FEATURE_CHOICE_IS, FOR_EACH_CHAR_IN_STRING, CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), CDeflineGenerator::ms_p_Low_Quality_Fsa, NCBI_SEQFEAT, and str().

Referenced by CDeflineGenerator::x_SetPrefix(), CDeflineGenerator::x_SetTitleFromProtein(), and CDeflineGenerator::x_SetTitleFromProteinIdx().

x_CountAmbigInRange()

void CSequenceAmbigTrimmer::x_CountAmbigInRange ( SAmbigCount &  out_result, const CSeqVector &  seqvec, const TSignedSeqPos  iStartPosInclusive_arg, const TSignedSeqPos  iEndPosInclusive_arg, const TSignedSeqPos  iTrimDirection  )

protectedvirtual

This counts the number of ambiguous bases in the range [leftmost_pos_to_check, rightmost_pos_to_check].

Note that rightmost_pos_to_check is inclusive.

Parameters

out_result	This will store the result. Pass in a struct initialized by the default constructor.
seqvec	This is used to get the bases.
iStartPosInclusive	This is where we start our count.
iEndPosInclusive	This is where we end our count. Note that it can be < or > iStartPosInclusive, depending on trim direction.
iTrimDirection	1 to trim from left to right, -1 to trim from right to left.

Definition at line 571 of file seq_trimmer.cpp.

References abs, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSequenceAmbigTrimmer::fFlags_DoNotTrimSeqGap, CSeqMap::FindSegment(), CSeqVector::GetScope(), CSeqVector::GetSeqMap(), CSeqVector::GetSequenceType(), CSeqMap_CI::GetType(), CSeqVector::IsNucleotide(), CSeqVector::IsProtein(), CSequenceAmbigTrimmer::m_arrNucAmbigLookupTable, CSequenceAmbigTrimmer::m_arrProtAmbigLookupTable, CSequenceAmbigTrimmer::m_fFlags, max(), min(), NCBI_USER_THROW_FMT, NULL, CSequenceAmbigTrimmer::SAmbigCount::num_ambig_bases, CSequenceAmbigTrimmer::SAmbigCount::pos_after_last_gap, CSequenceAmbigTrimmer::x_SegmentGetBeginningInclusive(), CSequenceAmbigTrimmer::x_SegmentGetEndInclusive(), and CSequenceAmbigTrimmer::x_SeqMapIterDoNext().

Referenced by CSequenceAmbigTrimmer::x_FindWhereToTrim().

x_DescribeClones()

void CDeflineGenerator::x_DescribeClones ( vector< CTempString > &  desc, string &  buf  )

private

Definition at line 1437 of file create_defline.cpp.

References buf, CTempString::empty(), CTempString::find(), CDeflineGenerator::m_Clone, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_HTGSPooled, CDeflineGenerator::m_HTGSUnfinished, NPOS, and NStr::NumericToString().

Referenced by CDeflineGenerator::x_SetTitleFromBioSrc(), CDeflineGenerator::x_SetTitleFromGPipe(), CDeflineGenerator::x_SetTitleFromSegSeq(), and CDeflineGenerator::x_SetTitleFromWGS().

x_EdgeSeqMapGapAdjust()

void CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust ( const CSeqVector &  seqvec, TSignedSeqPos &  in_out_uStartOfGoodBasesSoFar, const TSignedSeqPos  uEndOfGoodBasesSoFar, const TSignedSeqPos  iTrimDirection, const TSignedSeqPos  uChunkSize  )

protectedvirtual

This adjusts in_out_uStartOfGoodBasesSoFar if we're at a CSeqMap gap.

It does not notice ambiguous bases that are inside a normal sequence.

Parameters

seqvec	This is used to access information about the sequence.
in_out_uStartOfGoodBasesSoFar	This is the start of where we check for a gap. It will be updated to be past the gap, if a gap is found.
in_out_uRightmostGoodBaseSoFar	Analogous to in_out_uLeftmostGoodBaseSoFar. It's inclusive.
uEndOfGoodBasesSoFar	This limits how far this function may search (inclusive) when looking for the end of a gap segment.
iTrimDirection	1 to trim from left to right, -1 to trim from right to left.
uChunkSize	The gap size that we chop off must be a multiple of uChunkSize. We will chop off less if we would go more than 1 past the uEndOfGoodBasesSoFar. A uChunkSize of 1 means no chunking for obvious math reasons.

Definition at line 497 of file seq_trimmer.cpp.

References abs, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSequenceAmbigTrimmer::fFlags_DoNotTrimSeqGap, CSeqMap::FindSegment(), CSeqVector::GetScope(), CSeqVector::GetSeqMap(), CSeqMap_CI::GetType(), CSeqVector::IsNucleotide(), CSeqVector::IsProtein(), CSequenceAmbigTrimmer::m_arrNucAmbigLookupTable, CSequenceAmbigTrimmer::m_arrProtAmbigLookupTable, CSequenceAmbigTrimmer::m_fFlags, NCBI_USER_THROW, NULL, and CSequenceAmbigTrimmer::x_SegmentGetEndInclusive().

Referenced by CSequenceAmbigTrimmer::x_FindWhereToTrim().

x_ExpandPattern()

void CSeqSearch::x_ExpandPattern ( string &  sequence, string &  buffer, size_t  pos, TPatternInfo &  pat_info, TSearchFlags  flags  )

private

Definition at line 5090 of file sequence.cpp.

References buf, eBase_A, eBase_C, eBase_G, eBase_T, flags, i, sc_CharToEnum, sc_EnumToChar, and CSeqSearch::x_AddPattern().

Referenced by CSeqSearch::x_AddNucleotidePattern().

x_FindNextGapOnBioseq()

CBioseqGaps_CI::EFindNext CBioseqGaps_CI::x_FindNextGapOnBioseq ( const CBioseq_Handle &  bioseq_h, const TSeqPos  pos_to_start_looking, TSeqPos &  out_pos_of_gap, TSeqPos &  out_len_of_gap  ) const

protectedvirtual

This finds the next gap on the bioseq, starting at given pos.

Parameters

bioseq_h	the bioseq on which we're seeking the next relevant gap.
pos_to_start_looking	This is the position on bioseq_h to start looking for a relevant gap.
out_pos_of_gap	If a gap is found, this holds the 0-based position of the start of that gap. This is undefined if no gap was found.
out_len_of_gap	If a gap is found, this holds the length of the gap. This is undefined if no gap was found.

Returns

This indicates whether or not a relevant gap was found.

Definition at line 191 of file bioseqgaps_ci.cpp.

References CBioseq_Handle::eCoding_Iupac, CBioseqGaps_CI::eFindNext_Found, CBioseqGaps_CI::eFindNext_NotFound, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeqMap::FindSegment(), CSeqMap_CI::GetEndPosition(), CSeqVector::GetGapChar(), CBioseq_Handle::GetScope(), CSeqVector::GetSeqMap(), CSeqMap_CI::GetType(), NCBI_USER_THROW_FMT, and CSeqVector::size().

Referenced by CBioseqGaps_CI::x_Next().

x_FindWhereToTrim()

TSignedSeqPos CSequenceAmbigTrimmer::x_FindWhereToTrim ( const CSeqVector &  seqvec, const TSignedSeqPos  iStartPosInclusive_arg, const TSignedSeqPos  iEndPosInclusive_arg, TSignedSeqPos  iTrimDirection  )

protectedvirtual

This returns the last good base that won't be trimmed (note: last really means "first" when we're starting from the end)

Parameters

seqvec	This lets us explore the Bioseq to find out where to trim.
iStartPosInclusive_arg	This is the where we start our trimming. Depending on direction, this could be < or > iEndPosInclusive_arg.
iEndPosInclusive_arg	This is where the trimming ends (inclusive). Analogous to iStartPosInclusive_arg.
iTrimDirection	1 to trim from left to right, -1 to trim from right to left.

Returns

The last good base (remember: last means "lower number" when we're checking from the end). If trimming would trim off the entire sequence, it returns a position past the end of the sequence.

Definition at line 362 of file seq_trimmer.cpp.

References _ASSERT, abs, CSequenceAmbigTrimmer::STrimRule::bases_to_check, ITERATE, CSequenceAmbigTrimmer::m_uMinSeqLen, CSequenceAmbigTrimmer::m_vecTrimRules, max(), CSequenceAmbigTrimmer::STrimRule::max_bases_allowed_to_be_ambig, min(), CSequenceAmbigTrimmer::SAmbigCount::num_ambig_bases, CSequenceAmbigTrimmer::SAmbigCount::pos_after_last_gap, s_IsValidDirection(), CSequenceAmbigTrimmer::x_CountAmbigInRange(), and CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust().

Referenced by CSequenceAmbigTrimmer::DoTrim().

x_GetBestId()

void CFastaOstream::x_GetBestId ( CConstRef< CSeq_id > &  gi_id, CConstRef< CSeq_id > &  best_id, bool &  hide_prefix, const CBioseq &  bioseq  )

protectedvirtual

Definition at line 2812 of file sequence.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Other, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeq_inst_Base::eMol_aa, CSeq_id::FastaAARank(), CSeq_id::FastaNARank(), CFastaOstream::fEnableGI, CFastaOstream::fHideGenBankPrefix, FindBestChoice(), CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetMol(), ITERATE, CFastaOstream::m_Flags, CConstRef< C, Locker >::NotEmpty(), and CSeq_id_Base::Which().

Referenced by CFastaOstream::x_WriteAsFasta().

x_GetCurrent()

const CBioseqGaps_CI::SCurrentGapInfo & CBioseqGaps_CI::x_GetCurrent ( void  ) const

protectedvirtual

This gives info on the gap we're currently on.

Throws if this iterator has finished.

Definition at line 84 of file bioseqgaps_ci.cpp.

References CBioseqGaps_CI::m_infoOnCurrentGap, and NCBI_USER_THROW.

Referenced by CBioseqGaps_CI::operator*(), and CBioseqGaps_CI::operator->().

x_GetGeneRefViaCDS()

CConstRef< CGene_ref > CDeflineGenerator::x_GetGeneRefViaCDS ( const CMappedFeat &  mapped_cds )

private

Definition at line 1993 of file create_defline.cpp.

References CRef< C, Locker >::Empty(), FOR_EACH_SEQFEATXREF_ON_FEATURE, GetBestGeneForCds(), CSeq_feat_Base::GetData(), CSeqFeatXref_Base::GetData(), CSeqFeatData_Base::GetGene(), CMappedFeat::GetOriginalFeature(), CSeqFeatData_Base::IsGene(), CSeqFeatXref_Base::IsSetData(), CDeflineGenerator::m_ConstructedFeatTree, CDeflineGenerator::m_Feat_Tree, CDeflineGenerator::m_InitializedFeatTree, CDeflineGenerator::m_TopSEH, and CRef< C, Locker >::Reset().

Referenced by CDeflineGenerator::x_SetTitleFromProtein().

x_GetLongestProtein()

CConstRef< CSeq_feat > CDeflineGenerator::x_GetLongestProtein ( const CBioseq_Handle &  bsh )

private

Definition at line 1920 of file create_defline.cpp.

References CSeqFeatData_Base::e_Prot, eOverlap_Contained, CProt_ref_Base::eProcessed_not_set, FOR_EACH_SEQFEAT_ON_BIOSEQ_HANDLE, GetBestOverlappingFeat(), CSeq_feat_Base::GetData(), CBioseq_Handle::GetInst_Length(), GetLength(), CSeq_feat_Base::GetLocation(), CProt_ref_Base::GetProcessed(), CSeqFeatData_Base::GetProt(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqId(), CSeq_feat_Base::IsSetData(), CBioseq_Handle::IsSetInst(), CBioseq_Handle::IsSetInst_Length(), CSeq_feat_Base::IsSetLocation(), CProt_ref_Base::IsSetProcessed(), prot, and CSeq_loc::SetWhole().

Referenced by CDeflineGenerator::x_SetTitleFromProtein().

x_GetMaskingStates()

void CFastaOstream::x_GetMaskingStates ( TMSMap &  masking_states, const CSeq_id *  base_seq_id, const CSeq_loc *  location, CScope *  scope  )

private

Definition at line 3074 of file sequence.cpp.

Referenced by CFastaOstream::Write(), and CFastaOstream::WriteSequence().

x_GetModifiers()

string CDeflineGenerator::x_GetModifiers

(

const CBioseq_Handle &

handle

)

Definition at line 3432 of file create_defline.cpp.

References CDefLineJoiner::Add(), CPCRPrimerSet_Base::CanGet(), CPCRReactionSet_Base::CanGet(), CBioSource_Base::CanGetGenome(), CBioseq_Handle::CanGetInst_Topology(), DEFINE_STATIC_ARRAY_MAP, CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_chromatophore, CBioSource_Base::eGenome_chromoplast, CBioSource_Base::eGenome_cyanelle, CBioSource_Base::eGenome_hydrogenosome, CBioSource_Base::eGenome_kinetoplast, CBioSource_Base::eGenome_leucoplast, CBioSource_Base::eGenome_mitochondrion, CBioSource_Base::eGenome_plasmid_in_mitochondrion, CBioSource_Base::eGenome_plasmid_in_plastid, CBioSource_Base::eGenome_plastid, CBioSource_Base::eGenome_proplastid, CBioSource_Base::eGenome_unknown, CTempString::empty(), ERR_POST_X, COrgMod_Base::eSubtype_acronym, CSubSource_Base::eSubtype_altitude, COrgMod_Base::eSubtype_anamorph, COrgMod_Base::eSubtype_authority, COrgMod_Base::eSubtype_bio_material, COrgMod_Base::eSubtype_biotype, COrgMod_Base::eSubtype_biovar, COrgMod_Base::eSubtype_breed, CSubSource_Base::eSubtype_cell_line, CSubSource_Base::eSubtype_cell_type, COrgMod_Base::eSubtype_chemovar, CSubSource_Base::eSubtype_chromosome, CSubSource_Base::eSubtype_clone, CSubSource_Base::eSubtype_clone_lib, CSubSource_Base::eSubtype_collected_by, CSubSource_Base::eSubtype_collection_date, COrgMod_Base::eSubtype_common, CSubSource_Base::eSubtype_country, COrgMod_Base::eSubtype_cultivar, COrgMod_Base::eSubtype_culture_collection, CSubSource_Base::eSubtype_dev_stage, COrgMod_Base::eSubtype_dosage, COrgMod_Base::eSubtype_ecotype, CSubSource_Base::eSubtype_endogenous_virus_name, CSubSource_Base::eSubtype_environmental_sample, COrgMod_Base::eSubtype_forma, COrgMod_Base::eSubtype_forma_specialis, CSubSource_Base::eSubtype_frequency, COrgMod_Base::eSubtype_gb_acronym, COrgMod_Base::eSubtype_gb_anamorph, COrgMod_Base::eSubtype_gb_synonym, CSubSource_Base::eSubtype_genotype, CSubSource_Base::eSubtype_germline, COrgMod_Base::eSubtype_group, CSubSource_Base::eSubtype_haplogroup, CSubSource_Base::eSubtype_haplotype, CSubSource_Base::eSubtype_identified_by, CSubSource_Base::eSubtype_insertion_seq_name, COrgMod_Base::eSubtype_isolate, CSubSource_Base::eSubtype_isolation_source, CSubSource_Base::eSubtype_lab_host, CSubSource_Base::eSubtype_lat_lon, CSubSource_Base::eSubtype_linkage_group, CSubSource_Base::eSubtype_map, CSubSource_Base::eSubtype_mating_type, COrgMod_Base::eSubtype_metagenome_source, CSubSource_Base::eSubtype_metagenomic, COrgMod_Base::eSubtype_nat_host, COrgMod_Base::eSubtype_nomenclature, COrgMod_Base::eSubtype_other, CSubSource_Base::eSubtype_other, COrgMod_Base::eSubtype_pathovar, CSubSource_Base::eSubtype_phenotype, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_plastid_name, CSubSource_Base::eSubtype_pop_variant, CSubSource_Base::eSubtype_rearranged, CSubSource_Base::eSubtype_segment, COrgMod_Base::eSubtype_serogroup, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_serovar, CSubSource_Base::eSubtype_sex, COrgMod_Base::eSubtype_specimen_voucher, COrgMod_Base::eSubtype_strain, COrgMod_Base::eSubtype_sub_species, CSubSource_Base::eSubtype_subclone, COrgMod_Base::eSubtype_subgroup, COrgMod_Base::eSubtype_substrain, COrgMod_Base::eSubtype_subtype, COrgMod_Base::eSubtype_synonym, COrgMod_Base::eSubtype_teleomorph, CSubSource_Base::eSubtype_tissue_lib, CSubSource_Base::eSubtype_tissue_type, CSubSource_Base::eSubtype_transgenic, CSubSource_Base::eSubtype_transposon_name, COrgMod_Base::eSubtype_type, COrgMod_Base::eSubtype_type_material, COrgMod_Base::eSubtype_variety, CSubSource_Base::eSubtype_whole_replicon, CMolInfo_Base::eTech_barcode, CMolInfo_Base::eTech_both, CMolInfo_Base::eTech_composite_wgs_htgs, CMolInfo_Base::eTech_concept_trans, CMolInfo_Base::eTech_concept_trans_a, CMolInfo_Base::eTech_derived, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_fli_cdna, CMolInfo_Base::eTech_genemap, CMolInfo_Base::eTech_htc, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_physmap, CMolInfo_Base::eTech_seq_pept, CMolInfo_Base::eTech_seq_pept_homol, CMolInfo_Base::eTech_seq_pept_overlap, CMolInfo_Base::eTech_standard, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, CSeq_inst_Base::eTopology_circular, CPCRPrimerSet_Base::Get(), CPCRReactionSet_Base::Get(), GetBioSource(), COrgName_Base::GetGcode(), CBioSource_Base::GetGenome(), CBioseq_Handle::GetInst_Topology(), COrgName_Base::GetMgcode(), COrgName_Base::GetMod(), GetMolInfo(), CSubSource_Base::GetName(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetPcr_primers(), COrgName_Base::GetPgcode(), CBioSource_Base::GetSubtype(), CSubSource_Base::GetSubtype(), COrg_ref_Base::GetTaxname(), CMolInfo_Base::GetTech(), COrgName_Base::IsSetGcode(), COrgName_Base::IsSetMgcode(), COrgName_Base::IsSetMod(), CSubSource_Base::IsSetName(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), CBioSource_Base::IsSetPcr_primers(), COrgName_Base::IsSetPgcode(), CBioSource_Base::IsSetSubtype(), CSubSource_Base::IsSetSubtype(), COrg_ref_Base::IsSetTaxname(), CMolInfo_Base::IsSetTech(), ITERATE, CDefLineJoiner::Join(), kEmptyStr, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_MICompleteness, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, mod(), NCBI_COMPLETENESS, NULL, sc_TechArray, subname, Warning(), and CDeflineGenerator::x_SetBioSrc().

Referenced by CDeflineGenerator::GenerateDefline().

x_GetTitleFlags()

sequence::CDeflineGenerator::TUserFlags CFastaOstream::x_GetTitleFlags ( void  ) const

inlineprivate

Definition at line 2978 of file sequence.cpp.

x_Init()

void CDeflineGenerator::x_Init ( void  )

private

internal methods

Definition at line 148 of file create_defline.cpp.

Referenced by CDeflineGenerator::CDeflineGenerator().

x_IsAllowMismatch()

bool CSeqSearch::x_IsAllowMismatch ( TSearchFlags  flags ) const

inlineprivate

Definition at line 1270 of file sequence.hpp.

References CSeqSearch::fAllowMismatch, flags, and CSeqSearch::m_Flags.

Referenced by CSeqSearch::x_AddPattern().

x_IsComplete()

bool CDeflineGenerator::x_IsComplete ( ) const

private

Definition at line 3401 of file create_defline.cpp.

References CDeflineGenerator::m_MICompleteness, and NCBI_COMPLETENESS.

Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffix(), CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetTitleFromGPipe(), CDeflineGenerator::x_SetTitleFromNC(), CDeflineGenerator::x_SetTitleFromProtein(), and CDeflineGenerator::x_SetTitleFromProteinIdx().

x_IsExpandPattern()

bool CSeqSearch::x_IsExpandPattern ( TSearchFlags  flags ) const

inlineprivate

Definition at line 1267 of file sequence.hpp.

References CSeqSearch::fExpandPattern, flags, and CSeqSearch::m_Flags.

Referenced by CSeqSearch::x_AddNucleotidePattern().

x_IsJustTopStrand()

bool CSeqSearch::x_IsJustTopStrand ( TSearchFlags  flags ) const

inlineprivate

Definition at line 1264 of file sequence.hpp.

References CSeqSearch::fJustTopStrand, flags, and CSeqSearch::m_Flags.

Referenced by CSeqSearch::AddNucleotidePattern().

x_MapMask()

CConstRef< CSeq_loc > CFastaOstream::x_MapMask ( CSeq_loc_Mapper &  mapper, const CSeq_loc &  mask, const CSeq_id *  base_seq_id, CScope *  scope  )

private

Definition at line 3043 of file sequence.cpp.

x_Next()

void CBioseqGaps_CI::x_Next ( void  )

protectedvirtual

This moves this iterator to the next relevant gap.

Throws if this iterator has finished.

Definition at line 92 of file bioseqgaps_ci.cpp.

References _ASSERT, CBioseqGaps_CI::eFindNext_Found, CBioseq_Handle::GetAccessSeq_id_Handle(), kInvalidSeqPos, CBioseqGaps_CI::SCurrentGapInfo::length, CBioseqGaps_CI::m_bioseq_CI, CBioseqGaps_CI::m_infoOnCurrentGap, CBioseqGaps_CI::m_Params, CBioseqGaps_CI::Params::max_gap_len_to_ignore, CBioseqGaps_CI::Params::max_num_gaps_per_seq, NCBI_USER_THROW, CBioseqGaps_CI::SCurrentGapInfo::num_gaps_seen_so_far_on_this_seq, CBioseqGaps_CI::SCurrentGapInfo::num_seqs_seen_so_far, CBioseqGaps_CI::SCurrentGapInfo::seq_id, CBioseqGaps_CI::SCurrentGapInfo::start_pos, CBioseqGaps_CI::x_FindNextGapOnBioseq(), and CBioseqGaps_CI::x_NextBioseq().

Referenced by CBioseqGaps_CI::operator++().

x_NextBioseq()

void CBioseqGaps_CI::x_NextBioseq ( void  )

protectedvirtual

This advances m_bioseq_CI although it has extra logic to terminate m_bioseq_CI if we've exceeded the number of bioseqs we can look for.

Definition at line 175 of file bioseqgaps_ci.cpp.

References CBioseqGaps_CI::m_bioseq_CI, CBioseqGaps_CI::m_infoOnCurrentGap, CBioseqGaps_CI::m_Params, CBioseqGaps_CI::Params::max_num_seqs, and CBioseqGaps_CI::SCurrentGapInfo::num_seqs_seen_so_far.

Referenced by CBioseqGaps_CI::x_Next().

x_NormalizeVecTrimRules()

void CSequenceAmbigTrimmer::x_NormalizeVecTrimRules ( TTrimRuleVec &  vecTrimRules )

protectedvirtual

This prepares the vector of trimming rules to be used by the trimming algorithm.

For example, it eliminate duplicates and puts the rules in the correct order.

Parameters

vecTrimRules

Input and output.

Definition at line 284 of file seq_trimmer.cpp.

References CSequenceAmbigTrimmer::STrimRule::bases_to_check, ITERATE, CSequenceAmbigTrimmer::STrimRule::max_bases_allowed_to_be_ambig, NCBI_USER_THROW_FMT, remove_if(), and ct::sort().

Referenced by CSequenceAmbigTrimmer::CSequenceAmbigTrimmer().

x_OrganelleName()

const char * CDeflineGenerator::x_OrganelleName ( CBioSource::TGenome  genome ) const

private

Definition at line 323 of file create_defline.cpp.

References CTempString::empty(), kEmptyCStr, CDeflineGenerator::m_FastaFormat, CDeflineGenerator::m_IsWGS, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Taxname, NCBI_GENOME, result, and s_IsVirusOrPhage().

Referenced by CDeflineGenerator::x_SetBioSrc().

x_SegmentGetBeginningInclusive()

TSignedSeqPos CSequenceAmbigTrimmer::x_SegmentGetBeginningInclusive ( const CSeqMap_CI &  segment, const TSignedSeqPos  iTrimDirection  )

inlineprotected

This returns the (inclusive) position at the beginning of the segment.

Parameters

segment	This is the segment we're trying to find the beginning of.
iTrimDirection	This is which direction in which we're trimming. The beginning will be in the opposite direction.

Returns

This returns the (inclusive) position at the beginning of the given segment. As always, the definition of "beginning" depends on iTrimDirection.

Definition at line 1521 of file sequence.hpp.

References CSequenceAmbigTrimmer::x_SegmentGetEndInclusive().

Referenced by CSequenceAmbigTrimmer::x_CountAmbigInRange().

x_SegmentGetEndInclusive()

TSignedSeqPos CSequenceAmbigTrimmer::x_SegmentGetEndInclusive ( const CSeqMap_CI &  segment, const TSignedSeqPos  iTrimDirection  )

protected

This returns the (inclusive) position at the end of the segment currently at iStartPosInclusive_arg.

Parameters

segment	This is the segment we're trying to find the end of.
iTrimDirection	This is which direction in which we're trimming. The end of the segment will be found by looking in that direction.

Returns

This returns the (inclusive) position at the end of the given segment. The definition of "end" depends on iTrimDirection.

As always, the definition of "end" depends on iTrimDirection.

Definition at line 674 of file seq_trimmer.cpp.

References _ASSERT, CSeqMap_CI::GetEndPosition(), CSeqMap_CI::GetPosition(), and s_IsValidDirection().

Referenced by CSequenceAmbigTrimmer::x_CountAmbigInRange(), CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust(), and CSequenceAmbigTrimmer::x_SegmentGetBeginningInclusive().

x_SeqMapIterDoNext()

CSeqMap_CI & CSequenceAmbigTrimmer::x_SeqMapIterDoNext ( CSeqMap_CI &  in_out_segment_it, const TSignedSeqPos  iTrimDirection  )

protected

Returns the "next" segment.

The definition of "next" depends on iTrimDirection

Parameters

in_out_segment	Caller gives the current CSeqMap_CI, which will be returned adjusted in the trim direction.
iTrimDirection	The direction in which to increment. 1 means normal incrementing and -1 really means decrementing.

Returns

Reference to in_out_segment_it.

Definition at line 692 of file seq_trimmer.cpp.

References _ASSERT, and s_IsValidDirection().

Referenced by CSequenceAmbigTrimmer::x_CountAmbigInRange().

x_SetBioSrc()

void CDeflineGenerator::x_SetBioSrc ( const CBioseq_Handle &  bsh )

private

Definition at line 1264 of file create_defline.cpp.

References CSeqFeatData_Base::e_Biosrc, CTempString::empty(), NStr::EqualNocase(), FOR_EACH_ORGMOD_ON_BIOSOURCE, FOR_EACH_SUBSOURCE_ON_BIOSOURCE, CPartialOrgName_Base::Get(), COrgName_Base::C_Name::GetBinomial(), CSeqFeatData_Base::GetBiosrc(), CSeq_feat_Base::GetData(), CTaxElement_Base::GetFixed_level(), CBioSource_Base::GetGenome(), CBinomialOrgName_Base::GetGenus(), CTaxElement_Base::GetLevel(), COrgName_Base::GetName(), CSubSource_Base::GetName(), CBioSource::GetOrgname(), CMappedFeat::GetOriginalFeature(), COrgName_Base::C_Name::GetPartial(), CBinomialOrgName_Base::GetSpecies(), COrgMod_Base::GetSubname(), CBioSource::GetTaxname(), COrgName_Base::C_Name::IsBinomial(), COrgName_Base::C_Name::IsPartial(), CPartialOrgName_Base::IsSet(), CSeq_feat_Base::IsSetData(), CTaxElement_Base::IsSetFixed_level(), CBioSource_Base::IsSetGenome(), CBinomialOrgName_Base::IsSetGenus(), CTaxElement_Base::IsSetLevel(), COrgName_Base::IsSetName(), CSubSource_Base::IsSetName(), CBioSource::IsSetOrgname(), CBinomialOrgName_Base::IsSetSpecies(), COrgMod_Base::IsSetSubname(), CBioSource::IsSetTaxname(), ITERATE, CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Clone, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_Map, CDeflineGenerator::m_MetaGenomeSource, CDeflineGenerator::m_Multispecies, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Segment, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, NCBI_GENOME, NCBI_ORGMOD, NCBI_SUBSOURCE, CConstRef< C, Locker >::NotEmpty(), rapidjson::source, str(), SWITCH_ON_ORGMOD_CHOICE, SWITCH_ON_SUBSOURCE_CHOICE, and CDeflineGenerator::x_OrganelleName().

Referenced by CDeflineGenerator::GenerateDefline(), and CDeflineGenerator::x_GetModifiers().

x_SetBioSrcIdx()

void CDeflineGenerator::x_SetBioSrcIdx ( const CBioseq_Handle &  bsh )

private

Definition at line 1195 of file create_defline.cpp.

References CSeqFeatData_Base::e_Biosrc, FOR_EACH_SUBSOURCE_ON_BIOSOURCE, CSeqEntryIndex::GetBioseqIndex(), CBioseqIndex::GetBioSource(), CSeqFeatData_Base::GetBiosrc(), CBioseqIndex::GetBreed(), CBioseqIndex::GetChromosome(), CBioseqIndex::GetClone(), CBioseqIndex::GetCultivar(), CSeq_feat_Base::GetData(), CBioseqIndex::GetGenome(), CBioseqIndex::GetGenus(), CBioseqIndex::GetIsolate(), CBioseqIndex::GetLinkageGroup(), CBioseqIndex::GetMap(), CBioseqIndex::GetMetaGenomeSource(), CBioseqIndex::GetOrganelle(), CMappedFeat::GetOriginalFeature(), CBioseqIndex::GetPlasmid(), CBioseqIndex::GetSegment(), CBioseqIndex::GetSpecies(), CBioseqIndex::GetSpecimenVoucher(), CBioseqIndex::GetStrain(), CBioseqIndex::GetSubstrain(), CBioseqIndex::GetTaxname(), CBioseqIndex::HasClone(), CBioseqIndex::IsChromosome(), CBioseqIndex::IsMultispecies(), CBioseqIndex::IsPlasmid(), CSeq_feat_Base::IsSetData(), CSubSource_Base::IsSetName(), CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Clone, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_Map, CDeflineGenerator::m_MetaGenomeSource, CDeflineGenerator::m_Multispecies, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Segment, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, NCBI_SUBSOURCE, rapidjson::source, and SWITCH_ON_SUBSOURCE_CHOICE.

Referenced by CDeflineGenerator::GenerateDefline().

x_SetFlags()

void CDeflineGenerator::x_SetFlags ( const CBioseq_Handle &  bsh, TUserFlags  flags  )

private

Definition at line 612 of file create_defline.cpp.

References _ASSERT, _TROUBLE, CTempString::clear(), CSeqdesc_Base::e_Comment, CSeqdesc_Base::e_Embl, CSeqdesc_Base::e_Genbank, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Pdb, CSeqdesc_Base::e_Source, CSeqdesc_Base::e_Title, CSeqdesc_Base::e_User, CTempString::empty(), NStr::EqualNocase(), CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_map, CSeq_inst_Base::eRepr_seg, CSeq_inst_Base::eRepr_virtual, COrgMod_Base::eSubtype_metagenome_source, CSeq_id::fAcc_master, CDeflineGenerator::fAllProteinNames, CDeflineGenerator::fDevMode, CDeflineGenerator::fFastaFormat, CDeflineGenerator::fGpipeMode, FIELD_IS_SET_AND_IS, CDeflineGenerator::fIgnoreExisting, NStr::Find(), flags, CDeflineGenerator::fLocalAnnotsOnly, CDeflineGenerator::fOmitTaxonomicName, FOR_EACH_COMPOUND_ON_PDBBLOCK, FOR_EACH_SEQID_ON_BIOSEQ_HANDLE, FOR_EACH_STRING_IN_LIST, FOR_EACH_USERFIELD_ON_USEROBJECT, NStr::fSplit_Tokenize, CMap_ext_Base::Get(), CPartialOrgName_Base::Get(), GET_FIELD, CTextseq_id_Base::GetAccession(), CMolInfo_Base::GetBiomol(), CPDB_seq_id_Base::GetChain(), CPDB_seq_id_Base::GetChain_id(), CPatent_seq_id_Base::GetCit(), CMolInfo_Base::GetCompleteness(), CId_pat_Base::GetCountry(), CUser_field_Base::GetData(), CSeq_feat_Base::GetData(), CTaxElement_Base::GetFixed_level(), CObject_id_Base::GetId(), CBioseq_Handle::GetInst_Ext(), CBioseq_Handle::GetInst_Length(), CBioseq_Handle::GetInst_Repr(), CBioseq_Handle::GetInst_Topology(), CEMBL_block_Base::GetKeywords(), CGB_block_Base::GetKeywords(), CUser_field_Base::GetLabel(), CTaxElement_Base::GetLevel(), CSeq_ext_Base::GetMap(), COrgName_Base::GetMod(), COrgName_Base::GetName(), CTaxElement_Base::GetName(), CBioSource::GetOrgname(), COrgName_Base::C_Name::GetPartial(), CSeqFeatData_Base::GetRsite(), CSeq_id_Handle::GetSeqId(), CPatent_seq_id_Base::GetSeqid(), CId_pat::GetSomeNumber(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CRsite_ref_Base::GetStr(), CDbtag_Base::GetTag(), CMolInfo_Base::GetTech(), CUser_object_Base::GetType(), CSeq_id::IdentifyAccession(), CBioseq_Handle::IsAa(), CObject_id_Base::IsId(), CSeq_ext_Base::IsMap(), CBioseq_Handle::IsNa(), COrgName_Base::C_Name::IsPartial(), CSeqFeatData_Base::IsRsite(), CMap_ext_Base::IsSet(), CPartialOrgName_Base::IsSet(), CTextseq_id_Base::IsSetAccession(), CPDB_seq_id_Base::IsSetChain(), CPDB_seq_id_Base::IsSetChain_id(), CPatent_seq_id_Base::IsSetCit(), CUser_field_Base::IsSetData(), CTaxElement_Base::IsSetFixed_level(), CBioseq_Handle::IsSetInst(), CBioseq_Handle::IsSetInst_Ext(), CBioseq_Handle::IsSetInst_Repr(), CEMBL_block_Base::IsSetKeywords(), CGB_block_Base::IsSetKeywords(), CTaxElement_Base::IsSetLevel(), COrgName_Base::IsSetMod(), CTaxElement_Base::IsSetName(), CBioSource::IsSetOrgname(), CPatent_seq_id_Base::IsSetSeqid(), CDbtag_Base::IsSetTag(), CDbtag::IsSkippable(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), CRsite_ref_Base::IsStr(), CUser_object::IsUnreviewed(), CUser_object::IsUnreviewedUnannotated(), CUser_object::IsUnverified(), CUser_object::IsUnverifiedContaminant(), CUser_object::IsUnverifiedFeature(), CUser_object::IsUnverifiedMisassembled(), CUser_object::IsUnverifiedOrganism(), ITERATE, CDeflineGenerator::m_AllProtNames, CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Clone, CDeflineGenerator::m_Comment, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_DevMode, CDeflineGenerator::m_FastaFormat, CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_GeneralId, CDeflineGenerator::m_GeneralStr, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_GpipeMode, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_HTGSCancelled, CDeflineGenerator::m_HTGSDraft, CDeflineGenerator::m_HTGSPooled, CDeflineGenerator::m_HTGSUnfinished, CDeflineGenerator::m_HTGTech, CDeflineGenerator::m_IsAA, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_IsDelta, CDeflineGenerator::m_IsEST_STS_GSS, CDeflineGenerator::m_IsMap, CDeflineGenerator::m_IsNA, CDeflineGenerator::m_IsNC, CDeflineGenerator::m_IsNM, CDeflineGenerator::m_IsNR, CDeflineGenerator::m_IsNZ, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsPatent, CDeflineGenerator::m_IsPDB, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_IsPseudogene, CDeflineGenerator::m_IsSeg, CDeflineGenerator::m_IsTLS, CDeflineGenerator::m_IsTSA, CDeflineGenerator::m_IsUnreviewed, CDeflineGenerator::m_IsUnverified, CDeflineGenerator::m_IsVirtual, CDeflineGenerator::m_IsWGS, CDeflineGenerator::m_IsWP, CDeflineGenerator::m_Length, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Map, CDeflineGenerator::m_MetaGenomeSource, CDeflineGenerator::m_MIBiomol, CDeflineGenerator::m_MICompleteness, CDeflineGenerator::m_MITech, CDeflineGenerator::m_Multispecies, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_PatentCountry, CDeflineGenerator::m_PatentNumber, CDeflineGenerator::m_PatentSequence, CDeflineGenerator::m_PDBChain, CDeflineGenerator::m_PDBChainID, CDeflineGenerator::m_PDBCompound, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Reconstruct, CDeflineGenerator::m_rEnzyme, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Segment, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_TargetedLocus, CDeflineGenerator::m_Taxname, CDeflineGenerator::m_ThirdParty, CDeflineGenerator::m_TLSMaster, CDeflineGenerator::m_Topology, CDeflineGenerator::m_TPAExp, CDeflineGenerator::m_TPAInf, CDeflineGenerator::m_TPAReasm, CDeflineGenerator::m_TSAMaster, CDeflineGenerator::m_Unordered, CDeflineGenerator::m_UnreviewedPrefix, CDeflineGenerator::m_UnverifiedPrefix, CDeflineGenerator::m_UseBiosrc, CDeflineGenerator::m_UsePDBCompoundForDefline, CDeflineGenerator::m_WGSMaster, NCBI_ACCN, NCBI_BIOMOL, NCBI_COMPLETENESS, NCBI_GENOME, NCBI_SEQID, NCBI_SEQTOPOLOGY, NCBI_TECH, NPOS, NULL, CConstRef< C, Locker >::Reset(), NStr::Split(), str(), Type, and CSeq_id_Handle::Which().

Referenced by CDeflineGenerator::GenerateDefline().

x_SetFlagsIdx()

void CDeflineGenerator::x_SetFlagsIdx ( const CBioseq_Handle &  bsh, TUserFlags  flags  )

private

Definition at line 430 of file create_defline.cpp.

References CTempString::clear(), CTempString::empty(), CDeflineGenerator::fAllProteinNames, CDeflineGenerator::fDevMode, CDeflineGenerator::fFastaFormat, CDeflineGenerator::fGpipeMode, CDeflineGenerator::fIgnoreExisting, NStr::Find(), flags, CDeflineGenerator::fLocalAnnotsOnly, CDeflineGenerator::fOmitTaxonomicName, CBioseqIndex::GetBiomol(), CSeqEntryIndex::GetBioseqIndex(), CBioseqIndex::GetBioSource(), CBioseqIndex::GetBreed(), CBioseqIndex::GetChromosome(), CBioseqIndex::GetClone(), CBioseqIndex::GetComment(), CBioseqIndex::GetCompleteness(), CBioseqIndex::GetCultivar(), CBioseqIndex::GetFirstSuperKingdom(), CBioseqIndex::GetGeneralId(), CBioseqIndex::GetGeneralStr(), CBioseqIndex::GetGenome(), CBioseqIndex::GetGenus(), CBioseqIndex::GetIsolate(), CBioseqIndex::GetLength(), CBioseqIndex::GetLinkageGroup(), CBioseqIndex::GetMap(), CBioseqIndex::GetMetaGenomeSource(), CBioseqIndex::GetOrganelle(), CBioseqIndex::GetPatentCountry(), CBioseqIndex::GetPatentNumber(), CBioseqIndex::GetPatentSequence(), CBioseqIndex::GetPDBChain(), CBioseqIndex::GetPDBChainID(), CBioseqIndex::GetPDBCompound(), CBioseqIndex::GetPlasmid(), CBioseqIndex::GetrEnzyme(), CBioseqIndex::GetSecondSuperKingdom(), CBioseqIndex::GetSegment(), CBioseqIndex::GetSpecies(), CBioseqIndex::GetSpecimenVoucher(), CBioseqIndex::GetStrain(), CBioseqIndex::GetSubstrain(), CBioseqIndex::GetTargetedLocus(), CBioseqIndex::GetTaxname(), CBioseqIndex::GetTech(), CBioseqIndex::GetTitle(), CBioseqIndex::GetTopology(), CBioseqIndex::HasClone(), CBioseqIndex::IsAA(), CBioseqIndex::IsChromosome(), CBioseqIndex::IsCrossKingdom(), CBioseqIndex::IsDelta(), CBioseqIndex::IsEST_STS_GSS(), CBioseqIndex::IsHTGSCancelled(), CBioseqIndex::IsHTGSDraft(), CBioseqIndex::IsHTGSPooled(), CBioseqIndex::IsHTGSUnfinished(), CBioseqIndex::IsHTGTech(), CBioseqIndex::IsMap(), CBioseqIndex::IsMultispecies(), CBioseqIndex::IsNA(), CBioseqIndex::IsNC(), CBioseqIndex::IsNM(), CBioseqIndex::IsNR(), CBioseqIndex::IsNZ(), CBioseqIndex::IsPatent(), CBioseqIndex::IsPDB(), CBioseqIndex::IsPlasmid(), CBioseqIndex::IsPseudogene(), CBioseqIndex::IsThirdParty(), CBioseqIndex::IsTLS(), CBioseqIndex::IsTLSMaster(), CBioseqIndex::IsTPAExp(), CBioseqIndex::IsTPAInf(), CBioseqIndex::IsTPAReasm(), CBioseqIndex::IsTSA(), CBioseqIndex::IsTSAMaster(), CBioseqIndex::IsUnordered(), CBioseqIndex::IsUnreviewed(), CBioseqIndex::IsUnreviewedUnannotated(), CBioseqIndex::IsUnverified(), CBioseqIndex::IsUnverifiedContaminant(), CBioseqIndex::IsUnverifiedFeature(), CBioseqIndex::IsUnverifiedMisassembled(), CBioseqIndex::IsUnverifiedOrganism(), CBioseqIndex::IsUseBiosrc(), CBioseqIndex::IsVirtual(), CBioseqIndex::IsWGS(), CBioseqIndex::IsWGSMaster(), CBioseqIndex::IsWP(), CDeflineGenerator::m_AllProtNames, CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Clone, CDeflineGenerator::m_Comment, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_DevMode, CDeflineGenerator::m_FastaFormat, CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_GeneralId, CDeflineGenerator::m_GeneralStr, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Genus, CDeflineGenerator::m_GpipeMode, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_HTGSCancelled, CDeflineGenerator::m_HTGSDraft, CDeflineGenerator::m_HTGSPooled, CDeflineGenerator::m_HTGSUnfinished, CDeflineGenerator::m_HTGTech, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsAA, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_IsDelta, CDeflineGenerator::m_IsEST_STS_GSS, CDeflineGenerator::m_IsMap, CDeflineGenerator::m_IsNA, CDeflineGenerator::m_IsNC, CDeflineGenerator::m_IsNM, CDeflineGenerator::m_IsNR, CDeflineGenerator::m_IsNZ, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsPatent, CDeflineGenerator::m_IsPDB, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_IsPseudogene, CDeflineGenerator::m_IsSeg, CDeflineGenerator::m_IsTLS, CDeflineGenerator::m_IsTSA, CDeflineGenerator::m_IsUnreviewed, CDeflineGenerator::m_IsUnverified, CDeflineGenerator::m_IsVirtual, CDeflineGenerator::m_IsWGS, CDeflineGenerator::m_IsWP, CDeflineGenerator::m_Length, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Map, CDeflineGenerator::m_MetaGenomeSource, CDeflineGenerator::m_MIBiomol, CDeflineGenerator::m_MICompleteness, CDeflineGenerator::m_MITech, CDeflineGenerator::m_Multispecies, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_PatentCountry, CDeflineGenerator::m_PatentNumber, CDeflineGenerator::m_PatentSequence, CDeflineGenerator::m_PDBChain, CDeflineGenerator::m_PDBChainID, CDeflineGenerator::m_PDBCompound, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Reconstruct, CDeflineGenerator::m_rEnzyme, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Segment, CDeflineGenerator::m_Source, CDeflineGenerator::m_Species, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_TargetedLocus, CDeflineGenerator::m_Taxname, CDeflineGenerator::m_ThirdParty, CDeflineGenerator::m_TLSMaster, CDeflineGenerator::m_Topology, CDeflineGenerator::m_TPAExp, CDeflineGenerator::m_TPAInf, CDeflineGenerator::m_TPAReasm, CDeflineGenerator::m_TSAMaster, CDeflineGenerator::m_Unordered, CDeflineGenerator::m_UnreviewedPrefix, CDeflineGenerator::m_UnverifiedPrefix, CDeflineGenerator::m_UseBiosrc, CDeflineGenerator::m_UsePDBCompoundForDefline, CDeflineGenerator::m_WGSMaster, and NPOS.

Referenced by CDeflineGenerator::GenerateDefline().

x_SetPrefix()

void CDeflineGenerator::x_SetPrefix ( string &  prefix, const CBioseq_Handle &  bsh  )

private

Definition at line 2800 of file create_defline.cpp.

References CSeqEntryIndex::GetBioseqIndex(), CBioseqIndex::GetFeatureForProduct(), CFeatureIndex::GetMappedFeat(), CMappedFeat::GetOriginalFeature(), kEmptyCStr, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsAA, CDeflineGenerator::m_IsPseudogene, CDeflineGenerator::m_IsTLS, CDeflineGenerator::m_IsTSA, CDeflineGenerator::m_IsUnreviewed, CDeflineGenerator::m_IsUnverified, CDeflineGenerator::m_IsWP, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Multispecies, CDeflineGenerator::m_ThirdParty, CDeflineGenerator::m_TPAExp, CDeflineGenerator::m_TPAInf, CDeflineGenerator::m_TPAReasm, CDeflineGenerator::m_UnreviewedPrefix, CDeflineGenerator::m_UnverifiedPrefix, NPOS, prefix, and CDeflineGenerator::x_CDShasLowQualityException().

Referenced by CDeflineGenerator::GenerateDefline().

x_SetSuffix()

void CDeflineGenerator::x_SetSuffix ( string &  suffix, const CBioseq_Handle &  bsh, bool  appendComplete  )

private

Definition at line 2854 of file create_defline.cpp.

References CTempString::empty(), NStr::EqualNocase(), CSeqMap::fFindGap, NStr::IntToString(), CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Genome, CDeflineGenerator::m_HTGSCancelled, CDeflineGenerator::m_HTGSDraft, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_IsDelta, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_MIBiomol, CDeflineGenerator::m_MICompleteness, CDeflineGenerator::m_MITech, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_TargetedLocus, CDeflineGenerator::m_TLSMaster, CDeflineGenerator::m_TSAMaster, CDeflineGenerator::m_Unordered, CDeflineGenerator::m_WGSMaster, NCBI_BIOMOL, NCBI_COMPLETENESS, NCBI_GENOME, NCBI_TECH, NPOS, suffix, and type.

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromBioSrc()

void CDeflineGenerator::x_SetTitleFromBioSrc ( void  )

private

Definition at line 1545 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), CTempString::find(), ITERATE, CDefLineJoiner::Join(), CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Map, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, s_AddVoucherAndIsolate(), s_EndsWithStrain(), CTempString::substr(), NStr::TruncateSpacesInPlace(), and CDeflineGenerator::x_DescribeClones().

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromGPipe()

void CDeflineGenerator::x_SetTitleFromGPipe ( void  )

private

Definition at line 1865 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), CTempString::find(), NStr::FindNoCase(), ITERATE, CDefLineJoiner::Join(), CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_has_clone, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Map, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, NPOS, s_EndsWithStrain(), NStr::TruncateSpacesInPlace(), CDeflineGenerator::x_DescribeClones(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromMap()

void CDeflineGenerator::x_SetTitleFromMap ( void  )

private

Definition at line 2760 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), CTempString::find(), CDefLineJoiner::Join(), CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_rEnzyme, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, s_EndsWithStrain(), CTempString::substr(), and NStr::TruncateSpacesInPlace().

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromNC()

void CDeflineGenerator::x_SetTitleFromNC ( void  )

private

Definition at line 1603 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), CTempString::find(), NStr::FindNoCase(), CDefLineJoiner::Join(), CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Genome, CDeflineGenerator::m_IsChromosome, CDeflineGenerator::m_IsPlasmid, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_MIBiomol, CDeflineGenerator::m_Organelle, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_Segment, CDeflineGenerator::m_Taxname, NCBI_BIOMOL, NCBI_GENOME, NPOS, NStr::ReplaceInPlace(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromNM()

void CDeflineGenerator::x_SetTitleFromNM ( const CBioseq_Handle &  bsh )

private

Definition at line 1706 of file create_defline.cpp.

References CTextJoiner< num_prealloc, TIn, TOut >::Add(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Prot, CTempString::empty(), NStr::EqualNocase(), fFGL_Content, FOR_SELECTED_SEQFEAT_ON_BIOSEQ_HANDLE, GetLabel(), CBioseq_Handle::GetScope(), SAnnotSelector::IncludeFeatType(), CTextJoiner< num_prealloc, TIn, TOut >::Join(), CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Taxname, NStr::ReplaceInPlace(), CConstRef< C, Locker >::Reset(), SAnnotSelector::SetFeatType(), SAnnotSelector::SetResolveTSE(), SWITCH_ON_FEATURE_CHOICE, and x_FlyCG_PtoR().

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromNR()

void CDeflineGenerator::x_SetTitleFromNR ( const CBioseq_Handle &  bsh )

private

Definition at line 1762 of file create_defline.cpp.

References CTempString::empty(), fFGL_Content, FOR_EACH_SEQFEAT_ON_BIOSEQ_HANDLE, GetLabel(), CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_MIBiomol, CDeflineGenerator::m_Taxname, NCBI_BIOMOL, and string.

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromPatent()

void CDeflineGenerator::x_SetTitleFromPatent ( void  )

private

Definition at line 1819 of file create_defline.cpp.

References CTextJoiner< num_prealloc, TIn, TOut >::Add(), NStr::IntToString(), CTextJoiner< num_prealloc, TIn, TOut >::Join(), CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_PatentCountry, CDeflineGenerator::m_PatentNumber, and CDeflineGenerator::m_PatentSequence.

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromPDB()

void CDeflineGenerator::x_SetTitleFromPDB ( void  )

private

Definition at line 1829 of file create_defline.cpp.

References CTextJoiner< num_prealloc, TIn, TOut >::Add(), CTempString::find_first_not_of(), isprint(), CTextJoiner< num_prealloc, TIn, TOut >::Join(), CTempString::length(), CDeflineGenerator::m_Comment, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_PDBChain, CDeflineGenerator::m_PDBChainID, CDeflineGenerator::m_PDBCompound, CDeflineGenerator::m_UsePDBCompoundForDefline, and CTempString::substr().

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromProtein()

void CDeflineGenerator::x_SetTitleFromProtein ( const CBioseq_Handle &  bsh )

private

Definition at line 2387 of file create_defline.cpp.

References delta(), CTempString::empty(), NStr::EqualNocase(), CTempString::find(), NStr::FindNoCase(), FOR_EACH_ACTIVITY_ON_PROT, FOR_EACH_NAME_ON_PROT, FOR_EACH_SYNONYM_ON_GENE, CSeq_feat_Base::GetData(), CGene_ref_Base::GetDesc(), CProt_ref_Base::GetDesc(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), GetMappedCDSForProduct(), CMappedFeat::GetOriginalFeature(), CSeqFeatData_Base::GetProt(), CBioSource::GetTaxname(), CGene_ref_Base::IsSetDesc(), CProt_ref_Base::IsSetDesc(), CGene_ref_Base::IsSetLocus(), CGene_ref_Base::IsSetLocus_tag(), CBioSource::IsSetTaxname(), CDeflineGenerator::m_AllProtNames, CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_Genome, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Taxname, NCBI_GENOME, CConstRef< C, Locker >::NotEmpty(), NPOS, offset, prefix, prot, s_proteinOrganellePrefix, s_RemoveBracketedOrgFromEnd(), NStr::StartsWith(), str(), string, tmp, CDeflineGenerator::x_CDShasLowQualityException(), CDeflineGenerator::x_GetGeneRefViaCDS(), CDeflineGenerator::x_GetLongestProtein(), x_GetSourceFeatViaCDS(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromProteinIdx()

void CDeflineGenerator::x_SetTitleFromProteinIdx ( const CBioseq_Handle &  bsh )

private

Definition at line 2177 of file create_defline.cpp.

References delta(), CTempString::empty(), NStr::EqualNocase(), CTempString::find(), NStr::FindNoCase(), FOR_EACH_ACTIVITY_ON_PROT, FOR_EACH_NAME_ON_PROT, FOR_EACH_SYNONYM_ON_GENE, CFeatureIndex::GetBestGene(), CBioseqIndex::GetBestProteinFeature(), CSeqEntryIndex::GetBioseqIndex(), CSeq_feat_Handle::GetData(), CGene_ref_Base::GetDesc(), CProt_ref_Base::GetDesc(), CBioseqIndex::GetFeatureForProduct(), CSeqFeatData_Base::GetGene(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CFeatureIndex::GetMappedFeat(), CMappedFeat::GetOriginalFeature(), CSeqFeatData_Base::GetProt(), CBioSource::GetTaxname(), CGene_ref_Base::IsSetDesc(), CProt_ref_Base::IsSetDesc(), CGene_ref_Base::IsSetLocus(), CGene_ref_Base::IsSetLocus_tag(), CBioSource::IsSetTaxname(), CDeflineGenerator::m_AllProtNames, CDeflineGenerator::m_FirstSuperKingdom, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Idx, CDeflineGenerator::m_IsCrossKingdom, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_OmitTaxonomicName, CDeflineGenerator::m_SecondSuperKingdom, CDeflineGenerator::m_Taxname, NCBI_GENOME, CConstRef< C, Locker >::NotEmpty(), NPOS, offset, prefix, prot, s_proteinOrganellePrefix, s_RemoveBracketedOrgFromEnd(), NStr::StartsWith(), str(), string, tmp, CDeflineGenerator::x_CDShasLowQualityException(), x_GetSourceFeatViaCDS(), and CDeflineGenerator::x_IsComplete().

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromSegSeq()

void CDeflineGenerator::x_SetTitleFromSegSeq ( const CBioseq_Handle &  bsh )

private

Definition at line 2647 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), ITERATE, CDefLineJoiner::Join(), CDeflineGenerator::m_Clone, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_LocalAnnotsOnly, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Taxname, s_EndsWithStrain(), string, NStr::TruncateSpacesInPlace(), CDeflineGenerator::x_DescribeClones(), and x_GetSegSeqInfoViaCDS().

Referenced by CDeflineGenerator::GenerateDefline().

x_SetTitleFromWGS()

void CDeflineGenerator::x_SetTitleFromWGS ( void  )

private

Definition at line 2695 of file create_defline.cpp.

References CDefLineJoiner::Add(), eHideType, CTempString::empty(), CTempString::find(), ITERATE, CDefLineJoiner::Join(), CDeflineGenerator::m_Breed, CDeflineGenerator::m_Chromosome, CDeflineGenerator::m_Clone, CDeflineGenerator::m_Cultivar, CDeflineGenerator::m_GeneralId, CDeflineGenerator::m_GeneralStr, CDeflineGenerator::m_Genome, CDeflineGenerator::m_Isolate, CDeflineGenerator::m_IsWGS, CDeflineGenerator::m_LinkageGroup, CDeflineGenerator::m_MainTitle, CDeflineGenerator::m_Map, CDeflineGenerator::m_Plasmid, CDeflineGenerator::m_SpecimenVoucher, CDeflineGenerator::m_Strain, CDeflineGenerator::m_Substrain, CDeflineGenerator::m_Taxname, CDeflineGenerator::m_Topology, NCBI_GENOME, NCBI_SEQTOPOLOGY, NStr::NumericToString(), s_AddVoucherAndIsolate(), s_EndsWithStrain(), CTempString::substr(), tmp, NStr::TruncateSpacesInPlace(), and CDeflineGenerator::x_DescribeClones().

Referenced by CDeflineGenerator::GenerateDefline().

x_SliceBioseq()

void CSequenceAmbigTrimmer::x_SliceBioseq ( TSignedSeqPos  leftmost_good_base, TSignedSeqPos  rightmost_good_base, CBioseq_Handle &  bioseq_handle  )

protected

Definition at line 701 of file seq_trimmer.cpp.

References CInt_fuzz_Base::eLim_unk, CSeq_inst_Base::eRepr_raw, CSeq_inst_Base::eRepr_virtual, CSeqMap::eSeqData, CSeqMap::eSeqGap, eType, CSeqVector::GetCoding(), CBioseq_Handle::GetEditHandle(), CSeqMap_CI::GetEndPosition(), CBioseq_Handle::GetInst(), CSeqMap_CI::GetLength(), CSeqVector::GetPackedSeqData(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefGapLiteral(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CSeqMap_CI::GetType(), CSeqMap_CI::IsUnknownLength(), NCBI_USER_THROW_FMT, Ref(), CSeq_inst_Base::ResetExt(), CSeq_inst_Base::ResetSeq_data(), CSeqMap::ResolvedRangeIterator(), CAutoInitRef< T >::Set(), CSeq_inst_Base::SetExt(), CBioseq_EditHandle::SetInst(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetRepr(), and CSeq_inst_Base::SetSeq_data().

Referenced by CSequenceAmbigTrimmer::DoTrim().

x_StorePattern()

void CSeqSearch::x_StorePattern ( TPatternInfo &  pat_info, string &  sequence  )

private

Definition at line 5135 of file sequence.cpp.

References CSeqSearch::m_Fsa, and CSeqSearch::CPatternInfo::m_Sequence.

Referenced by CSeqSearch::x_AddPattern().

x_TestFlag()

bool CSequenceAmbigTrimmer::x_TestFlag ( TFlags  fFlag )

inlineprotected

Test if a given flag is set.

Definition at line 1392 of file sequence.hpp.

References CSequenceAmbigTrimmer::m_fFlags.

Referenced by CSequenceAmbigTrimmer::DoTrim().

x_TrimToNothing()

CSequenceAmbigTrimmer::EResult CSequenceAmbigTrimmer::x_TrimToNothing ( CBioseq_Handle &  bioseq_handle )

protectedvirtual

The bioseq is trimmed to size 0.

Parameters

bioseq_handle

The bioseq to trim to nothing.

Returns

Works just like the DoTrim return value.

Definition at line 340 of file seq_trimmer.cpp.

References CSeq_inst_Base::eRepr_virtual, CSequenceAmbigTrimmer::eResult_NoTrimNeeded, CSequenceAmbigTrimmer::eResult_SuccessfullyTrimmed, CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), CSeq_inst_Base::ResetExt(), CSeq_inst_Base::ResetSeq_data(), SerialClone(), CBioseq_EditHandle::SetInst(), CSeq_inst_Base::SetLength(), and CSeq_inst_Base::SetRepr().

Referenced by CSequenceAmbigTrimmer::DoTrim().

x_WriteAsFasta()

void CFastaOstream::x_WriteAsFasta ( const CBioseq &  bioseq )

protectedvirtual

Definition at line 2875 of file sequence.cpp.

References CFastaOstream::fEnableGI, CFastaOstream::fShowGnlAndAcc, CTextseq_id_Base::GetAccession(), CSeq_id::GetTextseq_Id(), CTextseq_id_Base::GetVersion(), CSeq_id_Base::IsGi(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetVersion(), CFastaOstream::m_Flags, CFastaOstream::m_Out, CConstRef< C, Locker >::NotEmpty(), s_WriteGnlAndAcc(), CSeq_id::WriteAsFasta(), and CFastaOstream::x_GetBestId().

x_WriteBuffer()

virtual void CFastaOstream::x_WriteBuffer ( const char *  buf, unsigned int  count  )

inlineprotectedvirtual

Reimplemented in CFastaOstreamEx.

Definition at line 904 of file sequence.hpp.

References buf.

Referenced by CFastaOstreamEx::x_WriteBuffer(), and CFastaOstream::x_WriteSequence().

x_WriteSeqIds()

void CFastaOstream::x_WriteSeqIds ( const CBioseq &  bioseq, const CSeq_loc *  location  )

protectedvirtual

Definition at line 2927 of file sequence.cpp.

References CFastaOstream::fNoDupCheck, CFastaOstream::fSuppressRange, CSeq_id_Handle::GetHandle(), CBioseq_Base::GetId(), set< Key, Compare >::insert(), ITERATE, location, CFastaOstream::m_Flags, CFastaOstream::m_PreviousWholeIds, NCBI_THROW, and NULL.

Referenced by CFastaOstream::Write().

x_WriteSeqTitle()

void CFastaOstream::x_WriteSeqTitle ( const CBioseq_Handle &  handle, const string &  custom_title  )

protectedvirtual

Definition at line 3000 of file sequence.cpp.

Referenced by CFastaOstream::Write().

x_WriteSequence()

void CFastaOstream::x_WriteSequence ( const CSeqVector &  vec, const TMSMap &  masking_state  )

private

Definition at line 3164 of file sequence.cpp.

References _ASSERT, CTempString::assign(), map_checker< Container >::begin(), CTempString::data(), CFastaOstream::eGM_count, CFastaOstream::eGM_dashes, CFastaOstream::eGM_letters, CFastaOstream::eGM_one_dash, CFastaOstream::eHardMask, map_checker< Container >::end(), CSeqMap::eSeqGap, CFastaOstream::eSoftMask, FIELD_IS_SET_AND_IS, CFastaOstream::fInstantiateGaps, CFastaOstream::fKeepUnknGapNomLen, CFastaOstream::fReverseStrand, CFastaOstream::fShowGapModifiers, CFastaOstream::fShowGapsOfSizeZero, AutoPtr< X, Del >::get(), CSeqVector_CI::GetBufferPtr(), CSeqVector_CI::GetBufferSize(), CSeqVector_CI::GetCurrentSeqMap_CI(),