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CDisplaySeqalign Class Reference

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#include <objtools/align_format/showalign.hpp>

+ Collaboration diagram for CDisplaySeqalign:

Classes

struct  DomainInfo
 structure for showing domains on the master sequence More...
 
struct  FeatureInfo
 structure for store feature display info More...
 
struct  SAlignTemplates
 
struct  SAlnDispParams
 
struct  SAlnFeatureInfo
 store feature information More...
 
struct  SAlnInfo
 store alnvec and score info More...
 
struct  SAlnLinksParams
 Info used to contstruct seq url obtained from processing the whole seq align for particular subject sequnce. More...
 
struct  SAlnRowInfo
 
struct  SAlnSeqlocInfo
 store seqloc info More...
 
struct  SInsertInformation
 internal insert information aln_start. More...
 

Public Types

enum  AlignType { eNotSet = 0 , eNuc = 1 , eProt = 2 }
 Alignment display type, specific for showing blast-related info. More...
 
enum  DisplayOption {
  eHtml = (1 << 0) , eLinkout = (1 << 1) , eSequenceRetrieval = (1 << 2) , eMergeAlign = (1 << 3) ,
  eShowMiddleLine = (1 << 4) , eShowGi = (1 << 6) , eShowIdentity = (1 << 7) , eShowBlastInfo = (1 << 8) ,
  eShowBlastStyleId = (1 << 9) , eNewTargetWindow = (1 << 10) , eShowCdsFeature = (1 << 11) , eShowGeneFeature = (1 << 12) ,
  eMasterAnchored = (1 << 13) , eColorDifferentBases = (1 << 14) , eTranslateNucToNucAlignment = (1 << 15) , eShowBl2seqLink = (1 << 16) ,
  eDynamicFeature = (1 << 17) , eShowNoDeflineInfo = (1 << 18) , eHyperLinkSlaveSeqid = (1 << 19) , eHyperLinkMasterSeqid = (1 << 20) ,
  eDisplayTreeView = (1 << 21) , eShowInfoOnMouseOverSeqid = (1 << 22) , eShowSortControls = (1 << 23) , eShowGeneInfo = (1 << 24) ,
  eShowCheckBox = (1 << 25) , eShowEndGaps = (1 << 26) , eShowGapOnlyLines = (1 << 27) , eShowRawScoreOnly = (1 << 28) ,
  eShowTranslationForLocalSeq = (1 << 29) , eShowAlignStatsForMultiAlignView = (1 << 30) , eShowSequencePropertyLabel = (1 << 31)
}
 option for alignment display More...
 
enum  TranslatedFrameForLocalSeq { eFirst = 0 , eSecond , eThird }
 
enum  MiddleLineStyle { eChar = 0 , eBar }
 Middle line style option. More...
 
enum  SeqLocCharOption { eX = 0 , eN , eLowerCase }
 character used to display seqloc, such as masked sequence More...
 
enum  SeqLocColorOption { eBlack = 0 , eGrey , eRed }
 colors for seqloc display More...
 
enum  LinksDisplayParams { eDisplayDefault = 0 , eDisplayResourcesLinks = (1 << 0) , eDisplayDownloadLink = (1 << 1) }
 

Public Member Functions

void SetTranslatedFrameForLocalSeq (TranslatedFrameForLocalSeq frame)
 
 CDisplaySeqalign (const objects::CSeq_align_set &seqalign, objects::CScope &scope, list< CRef< CSeqLocInfo > > *mask_seqloc=NULL, list< FeatureInfo * > *external_feature=NULL, const char *matrix_name="BLOSUM62")
 Constructors. More...
 
virtual ~CDisplaySeqalign ()
 Destructor. More...
 
void DisplaySeqalign (CNcbiOstream &out)
 call this to display seqalign More...
 
void SetLinkoutDB (ILinkoutDB *l, const string &mv_build_name)
 Set the linkout implementation. More...
 
void DisplayPairwiseSeqalign (CNcbiOstream &out, unordered_set< string > selectedIDs)
 
void SetAlignOption (int option)
 Set functions. More...
 
void SetSeqLocChar (SeqLocCharOption option=eX)
 character style for seqloc display such as masked region More...
 
void SetSeqLocColor (SeqLocColorOption option=eBlack)
 color for seqloc display such as masked region More...
 
void SetLineLen (size_t len)
 number of bases or amino acids per line More...
 
void SetNumAlignToShow (int num)
 Display top num seqalign Note this only limit the number of seqalign regardless of the seqids. More...
 
void SetMiddleLineStyle (MiddleLineStyle option=eBar)
 set middle line style More...
 
void SetMasterGeneticCode (int code)
 Set genetic code for master sequence. More...
 
void SetSlaveGeneticCode (int code)
 Set Genetic cod for slaves. More...
 
void SetAlignType (AlignType type)
 Needed only if you want to display positives and strand. More...
 
void SetDbName (string name)
 set blast database name More...
 
void SetDbType (bool is_na)
 database type. More...
 
void SetRid (string rid)
 set blast request id More...
 
void SetCddRid (string cdd_rid)
 CDD rid for constructing linkout. More...
 
void SetEntrezTerm (string term)
 for constructing structure linkout More...
 
void SetQueryNumber (int number)
 for linking to mapviewer More...
 
void SetBlastType (string type)
 internal blast type More...
 
void SetAlignSeqListIndex (int alignSeqListIndex)
 Set subject seq index. More...
 
void SetSubjectMasks (const TSeqLocInfoVector &masks)
 Sets the masks and the masking algorithm used for the subject sequences. More...
 
void SetCgiContext (CCgiContext &ctx)
 
void SetPreComputedResID (string preComputedResID)
 Sets CDD precomputed results ID. More...
 
void UseLongSequenceIds (void)
 Sets usage of long sequence ids (database|accession) More...
 
void SetQueryAnchoredIndex (int queryAnchoredSetIndex)
 Sets index of Query anchored alignment set to display or download. More...
 
void SetAlignTemplates (SAlignTemplates *alignTemplates)
 
void SetMasterDomain (list< CRef< DomainInfo > > *domain)
 
void SetSequencePropertyLabel (const vector< string > *SequencePropertyLabel, EOwnership ownership=eNoOwnership)
 
void SetResultPositionIndex (int index)
 

Static Public Member Functions

static CRef< objects::CSeq_align_set > PrepareBlastUngappedSeqalign (const objects::CSeq_align_set &alnset)
 static functions Need to call this if the seqalign is stdseg or dendiag for ungapped blast alignment display as each stdseg ro dendiag is a distinct alignment. More...
 
static CRef< objects::CSeq_align_set > PrepareBlastUngappedSeqalignEx (const objects::CSeq_align_set &alnset)
 static functions same as PrepareBlastUngappedSeqalign, but process seg scores uniformly even if there is only a single seg. More...
 
static CRef< objects::CSeq_align_set > PrepareBlastUngappedSeqalignEx2 (objects::CSeq_align_set &alnset)
 same as PrepareBlastUngappedSeqalign2, but sets aggregate scores. More...
 

Protected Types

typedef list< CRef< SInsertInformation > > TSInsertInformationList
 
typedef list< CRef< SAlnFeatureInfo > > TSAlnFeatureInfoList
 
typedef list< CRef< SAlnSeqlocInfo > > TSAlnSeqlocInfoList
 List of SAlnSeqlocInfo structures. More...
 
typedef map< SSeqIdKey, TMaskedQueryRegionsTSubjectMaskMap
 Definition of std::map of objects::CSeq_ids to masks. More...
 

Protected Member Functions

string x_PrintDynamicFeatures (void)
 
void x_DisplayAlnvec (CNcbiOstream &out)
 Display the current alnvec. More...
 
string x_PrintDefLine (const objects::CBioseq_Handle &bsp_handle, SAlnInfo *aln_vec_info)
 print defline More...
 
void x_OutputSeq (string &sequence, const objects::CSeq_id &id, int start, int len, int frame, int row, bool color_mismatch, const TSAlnSeqlocInfoList &loc_list, CNcbiOstream &out) const
 display sequence for one row More...
 
int x_GetNumGaps ()
 Count number of total gaps. More...
 
CAlignFormatUtil::SSeqURLInfox_InitSeqUrl (TGi giToUse, string accession, TTaxId taxid, const list< CRef< objects::CSeq_id > > &ids)
 get url to sequence record More...
 
string x_HTMLSeqIDLink (SAlnRowInfo *alnRoInfo, int row, TGi giToUse)
 
void x_InitAlignLinks (SAlnDispParams *alnDispParams, const list< CRef< objects::CBlast_def_line > > &bdl_list, int lnkDispPrarms)
 
string x_GetDumpgnlLink (const list< CRef< objects::CSeq_id > > &ids) const
 get dumpgnl url to sequence record More...
 
void x_GetFeatureInfo (TSAlnFeatureInfoList &feature, int custom_genetic_code, objects::CScope &scope, objects::CSeqFeatData::E_Choice choice, int row, string &sequence, list< list< CRange< TSeqPos > > > &feat_seq_range, list< objects::ENa_strand > &feat_seq_strand, bool fill_feat_range) const
 get feature info More...
 
void x_FillInserts (int row, objects::CAlnMap::TSignedRange &aln_range, int aln_start, list< string > &inserts, string &insert_pos_string, TSInsertInformationList &insert_list) const
 get inserts info More...
 
void x_DoFills (int row, objects::CAlnMap::TSignedRange &aln_range, int aln_start, TSInsertInformationList &insert_list, list< string > &inserts) const
 recusively fill the insert for anchored view More...
 
string x_GetSegs (int row) const
 segments starts and stops used for map viewer, etc More...
 
void x_FillIdentityInfo (const string &sequence_standard, const string &sequence, int &match, int &positive, string &middle_line)
 compute number of identical and positive residues and set middle line accordingly More...
 
void x_SetFeatureInfo (CRef< SAlnFeatureInfo > feat_info, const objects::CSeq_loc &seqloc, int aln_from, int aln_to, int aln_stop, char pattern_char, string pattern_id, string &alternative_feat_str, int genetic_code) const
 set feature info More...
 
void x_GetInserts (TSInsertInformationList &insert_list, objects::CAlnMap::TSeqPosList &insert_aln_start, objects::CAlnMap::TSeqPosList &insert_seq_start, objects::CAlnMap::TSeqPosList &insert_length, int line_aln_stop)
 get insert information More...
 
string x_GetGeneLinkUrl (int gene_id)
 get the URL of the Gene info link. More...
 
void x_DisplayAlnvecInfo (CNcbiOstream &out, SAlnInfo *aln_vec_info, bool show_defline)
 display alnvec info More...
 
void x_PrintDynamicFeatures (CNcbiOstream &out, SAlnInfo *aln_vec_info)
 output dynamic feature url More...
 
void x_FillLocList (TSAlnSeqlocInfoList &loc_list, const list< CRef< CSeqLocInfo > > *masks) const
 convert the passed seqloc list info using alnment coordinates More...
 
void x_GetQueryFeatureList (int row_num, int aln_stop, vector< TSAlnFeatureInfoList > &features) const
 get external query feature info such as phi blast pattern More...
 
void x_FillSeqid (string &id, int row) const
 make the appropriate seqid More...
 
int x_GetLinkout (const objects::CSeq_id &id)
 
void x_PrintFeatures (SAlnRowInfo *alnRoInfo, int row, string &master_feat_str, CNcbiOstream &out)
 print out features and fill master_feat_str if applicable More...
 
CRef< objects::CAlnVec > x_GetAlnVecForSeqalign (const objects::CSeq_align &align)
 
void x_DisplayBl2SeqLink (CNcbiOstream &out)
 Dipslay Bl2seq TBLASTX link. More...
 
void x_DisplayMpvAnchor (CNcbiOstream &out, SAlnInfo *aln_vec_info)
 Display anchor for links from mapview. More...
 
void x_DisplayAlignSortInfo (CNcbiOstream &out, string id_label)
 Display Sorting controls. More...
 
void x_DisplayAlignInfo (CNcbiOstream &out, SAlnInfo *aln_vec_info)
 Display score,bits,expect,method. More...
 
virtual string x_DisplayRowData (SAlnRowInfo *alnRoInfo)
 Display pairwise alignment. More...
 
virtual void x_DisplayRowData (SAlnRowInfo *alnRoInfo, CNcbiOstream &out)
 
string x_DisplayRowDataSet (SAlnRowInfo *alnRoInfo, int aln_start, vector< int > &prev_stop)
 
void x_ProcessRowDataSet (SAlnRowInfo *alnRoInfo, int aln_start, vector< int > &prev_stop)
 
void x_DisplayIdentityInfo (SAlnRowInfo *alnRoInfo, CNcbiOstream &out)
 Display identities,positives,frames etc. More...
 
void x_DisplaySingleAlignParams (CNcbiOstream &out, SAlnInfo *aln_vec_info, bool showSortControls)
 Display Sorting controls,score,bits,expect,method,features identities,positives,frames etc. More...
 
void x_PrepareIdentityInfo (SAlnInfo *aln_vec_info)
 
void x_PrepareDynamicFeatureInfo (SAlnInfo *aln_vec_info)
 Calculate data for feature display. More...
 
SAlnRowInfox_PrepareRowData (void)
 Calculate data for pairwise alignment display. More...
 
string x_FormatSingleAlign (SAlnInfo *aln_vec_info)
 
string x_FormatAlignSortInfo ()
 
string x_FormatAlnBlastInfo (SAlnInfo *aln_vec_info)
 
string x_FormatIdentityInfo (string alignInfo, SAlnInfo *aln_vec_info)
 
string x_FormatDynamicFeaturesInfo (string alignInfo, SAlnInfo *aln_vec_info)
 
string x_FormatOneDynamicFeature (string viewerURL, TGi subjectGi, int fromRange, int toRange, string featText)
 
void x_PreProcessSeqAlign (objects::CSeq_align_set &actual_aln_list)
 Sets m_Segs,m_HspNumber. More...
 
void x_CalcUrlLinksParams (const objects::CSeq_align &align, string idString, string toolUrl)
 
void x_DisplayAlnvecInfoHead (CNcbiOstream &out, SAlnInfo *aln_vec_info)
 
void x_InitAlignParams (objects::CSeq_align_set &actual_aln_list)
 Inits align parameters for displaySetup scope for feature fetching and m_DynamicFeature inits m_FeatObj,m_featScope,m_CanRetrieveSeq,m_ConfigFile,m_Reg,m_LinkoutOrder,m_DynamicFeature. More...
 
void x_PreProcessSingleAlign (objects::CSeq_align_set::Tdata::const_iterator currSeqAlignIter, objects::CSeq_align_set &actual_aln_list, bool multipleSeqs)
 
string x_FormatAlnHSPLinks (string &alignInfo)
 
SAlnDispParamsx_FillAlnDispParams (const CRef< objects::CBlast_def_line > &iter, const objects::CBioseq_Handle &bsp_handle, list< string > &use_this_seqid, TGi firstGi, int numLinkoutReads)
 
SAlnDispParamsx_FillAlnDispParams (const objects::CBioseq_Handle &bsp_handle)
 
string x_FormatDefLinesHeader (const objects::CBioseq_Handle &bsp_handle, SAlnInfo *aln_vec_info)
 
string x_InitDefLinesHeader (const objects::CBioseq_Handle &bsp_handle, SAlnInfo *aln_vec_info)
 
string x_MapDefLine (SAlnDispParams *alnDispParams, bool isFisrt, bool linkout, bool hideDefline, int seqLength)
 
void x_ShowAlnvecInfoTemplate (CNcbiOstream &out, SAlnInfo *aln_vec_info, bool show_defline)
 
void x_ShowAlnvecInfo (CNcbiOstream &out, SAlnInfo *aln_vec_info, bool show_defline)
 
void x_GetDomainInfo (int row_num, int aln_stop, vector< TSAlnFeatureInfoList > &retval) const
 
void x_AddTranslationForLocalSeq (vector< TSAlnFeatureInfoList > &retval, vector< string > &sequence) const
 
void x_DisplaySequenceIDForQueryAnchored (SAlnRowInfo *alnRoInfo, int row, CNcbiOstrstream &out)
 
void x_DisplaySequenceIDForPairwise (SAlnRowInfo *alnRoInfo, int row, bool has_mismatch, CNcbiOstrstream &out)
 
void x_DisplayInsertsForQueryAnchored (SAlnRowInfo *alnRoInfo, int row, CNcbiOstrstream &out)
 
void x_DisplaySequenceLine (SAlnRowInfo *alnRoInfo, int row, int prev_stop, CNcbiOstrstream &out)
 
void x_DisplayMiddLine (SAlnRowInfo *alnRoInfo, int row, CNcbiOstrstream &out)
 

Static Protected Member Functions

static TGi x_GetGiForSeqIdList (const list< CRef< objects::CSeq_id > > &ids)
 

Protected Attributes

TSubjectMaskMap m_SubjectMasks
 Map of subject masks. More...
 
CConstRef< objects::CSeq_align_set > m_SeqalignSetRef
 reference to seqalign set More...
 
list< CRef< CSeqLocInfo > > * m_Seqloc
 display character option for list of seqloc More...
 
list< FeatureInfo * > * m_QueryFeature
 external feature such as phiblast More...
 
list< CRef< DomainInfo > > * m_DomainInfo
 
AutoPtr< const vector< string > > m_SeqPropertyLabel
 
objects::CScope & m_Scope
 
objects::CAlnVec * m_AV
 
int ** m_Matrix
 
int m_AlignOption
 
AlignType m_AlignType
 
int m_NumAlignToShow
 
SeqLocCharOption m_SeqLocChar
 
SeqLocColorOption m_SeqLocColor
 
size_t m_LineLen
 
bool m_IsDbNa
 
bool m_CanRetrieveSeq
 
string m_DbName
 
string m_BlastType
 
string m_LinkoutOrder
 
string m_Rid
 
string m_CddRid
 
string m_EntrezTerm
 
int m_QueryNumber
 
CNcbiIfstreamm_ConfigFile
 
CNcbiRegistrym_Reg
 
objects::CGetFeature * m_DynamicFeature
 
map< string, struct SAlnLinksParamsm_AlnLinksParams
 
list< stringm_CustomLinksList
 
list< stringm_LinkoutList
 
list< stringm_HSPLinksList
 
string m_FASTAlinkUrl
 
string m_AlignedRegionsUrl
 
CAlignFormatUtil::SLinkoutInfo m_LinkoutInfo
 
CRef< objects::CObjectManager > m_FeatObj
 
CRef< objects::CScope > m_featScope
 
MiddleLineStyle m_MidLineStyle
 
int m_MasterGeneticCode
 
int m_SlaveGeneticCode
 
CCgiContextm_Ctx
 
SAlignTemplatesm_AlignTemplates
 
int m_cur_align
 Gene info reader object, reads Gene info entries from files. More...
 
int m_NumBlastDefLines
 Number of subject sequence deflines. More...
 
int m_currAlignHsp
 Current HSP number for single alignmnet. More...
 
int m_currAlignSeqListIndex
 Current subject seq index in descriptions table. More...
 
string m_PreComputedResID
 CDD precomputed results ID. More...
 
ILinkoutDBm_LinkoutDB
 Reference to LinkoutDB implementation. Not owned by this class. More...
 
string m_MapViewerBuildName
 mapviewer build name associated with the sequences in the BLAST database out of which the results are being formatted by this class. More...
 
string m_CurrAlnID_Lbl
 gi(if exists) that is used for html formatting otherwise id without db part More...
 
string m_CurrAlnAccession
 accession that is displayed More...
 
string m_CurrAlnID_DbLbl
 gi(if exists) that is used for html formatting otherwise id with db part like ti:xxxxxxx or GNOMON:XXXXXX More...
 
int m_TotalHSPNum
 
TranslatedFrameForLocalSeq m_TranslatedFrameForLocalSeq
 
int m_ResultPositionIndex
 result position index for multiple query case More...
 
bool m_UseLongSeqIds
 print long sequence ids (with gi and accession with database source) More...
 
int m_QueryAnchoredSetIndex
 

Private Member Functions

 CDisplaySeqalign (const CDisplaySeqalign &other)
 Prohibit copy constructor. More...
 
CDisplaySeqalignoperator= (const CDisplaySeqalign &rhs)
 Prohibit assignment operator. More...
 

Detailed Description

Definition at line 91 of file showalign.hpp.

Member Typedef Documentation

◆ TSAlnFeatureInfoList

Definition at line 496 of file showalign.hpp.

◆ TSAlnSeqlocInfoList

List of SAlnSeqlocInfo structures.

Definition at line 505 of file showalign.hpp.

◆ TSInsertInformationList

Definition at line 486 of file showalign.hpp.

◆ TSubjectMaskMap

Definition of std::map of objects::CSeq_ids to masks.

Definition at line 598 of file showalign.hpp.

Member Enumeration Documentation

◆ AlignType

Alignment display type, specific for showing blast-related info.

Enumerator
eNotSet 
eNuc 
eProt 

Definition at line 98 of file showalign.hpp.

◆ DisplayOption

option for alignment display

Enumerator
eHtml 
eLinkout 
eSequenceRetrieval 
eMergeAlign 
eShowMiddleLine 
eShowGi 
eShowIdentity 
eShowBlastInfo 
eShowBlastStyleId 
eNewTargetWindow 
eShowCdsFeature 
eShowGeneFeature 
eMasterAnchored 
eColorDifferentBases 
eTranslateNucToNucAlignment 
eShowBl2seqLink 
eDynamicFeature 
eShowNoDeflineInfo 
eHyperLinkSlaveSeqid 
eHyperLinkMasterSeqid 
eDisplayTreeView 
eShowInfoOnMouseOverSeqid 
eShowSortControls 
eShowGeneInfo 
eShowCheckBox 
eShowEndGaps 
eShowGapOnlyLines 
eShowRawScoreOnly 
eShowTranslationForLocalSeq 
eShowAlignStatsForMultiAlignView 
eShowSequencePropertyLabel 

Definition at line 122 of file showalign.hpp.

◆ LinksDisplayParams

Enumerator
eDisplayDefault 
eDisplayResourcesLinks 
eDisplayDownloadLink 

Definition at line 219 of file showalign.hpp.

◆ MiddleLineStyle

Middle line style option.

Enumerator
eChar 
eBar 

Definition at line 196 of file showalign.hpp.

◆ SeqLocCharOption

character used to display seqloc, such as masked sequence

Enumerator
eX 
eN 
eLowerCase 

Definition at line 203 of file showalign.hpp.

◆ SeqLocColorOption

colors for seqloc display

Enumerator
eBlack 
eGrey 
eRed 

Definition at line 212 of file showalign.hpp.

◆ TranslatedFrameForLocalSeq

Enumerator
eFirst 
eSecond 
eThird 

Definition at line 185 of file showalign.hpp.

Constructor & Destructor Documentation

◆ CDisplaySeqalign() [1/2]

CDisplaySeqalign::CDisplaySeqalign ( const objects::CSeq_align_set &  seqalign,
objects::CScope &  scope,
list< CRef< CSeqLocInfo > > *  mask_seqloc = NULL,
list< FeatureInfo * > *  external_feature = NULL,
const char *  matrix_name = "BLOSUM62" 
)

Constructors.

Parameters
seqalignseqalign to display.
mask_seqlocseqloc to be displayed with different characters and colors such as masked sequence.
external_featureFeature to display such as phiblast pattern. Must be seqloc-int
matrix_namescoring matrix name [in]
scopescope to fetch your sequence

◆ ~CDisplaySeqalign()

CDisplaySeqalign::~CDisplaySeqalign ( )
virtual

Destructor.

Definition at line 226 of file showalign.cpp.

References i, k_NumAsciiChar, m_ConfigFile, m_DynamicFeature, m_Matrix, and m_Reg.

◆ CDisplaySeqalign() [2/2]

CDisplaySeqalign::CDisplaySeqalign ( const CDisplaySeqalign other)
private

Prohibit copy constructor.

Member Function Documentation

◆ DisplayPairwiseSeqalign()

void CDisplaySeqalign::DisplayPairwiseSeqalign ( CNcbiOstream out,
unordered_set< string selectedIDs 
)

Definition at line 4680 of file showalign.cpp.

◆ DisplaySeqalign()

void CDisplaySeqalign::DisplaySeqalign ( CNcbiOstream out)

call this to display seqalign

Parameters
outstream for display

Definition at line 1915 of file showalign.cpp.

References _TRACE, ConstBegin(), CAlignFormatUtil::CreateDensegFromDendiag(), CSeq_align::CreateDensegFromStdseg(), CSeq_data_Base::e_Ncbieaa, CSeq_align_Base::C_Segs::e_Std, eHtml, eMergeAlign, CRef< C, Locker >::Empty(), CConstRef< C, Locker >::Empty(), eNa_strand_minus, eSequenceRetrieval, eSerial_AsnText, eTranslateNucToNucAlignment, eUnknown, CAlignFormatUtil::ExtractSeqalignSetFromDiscSegs(), CAlnMix::fFillUnalignedRegions, CAlnMix::fForceTranslation, CAlnMix::fMinGap, CAlnMix::fNegativeStrand, CAlnMix::fPreserveRows, CAlnMix::fQuerySeqMergeOnly, Get(), CSeq_align_set_Base::Get(), CAlignFormatUtil::GetAlnScores(), CAlnVec::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetSegs(), CAlnMap::GetSeqId(), GetSeqIdString(), CDense_seg::GetWidths(), i, int, CDense_seg::IsSetWidths(), k_FrameConversion, k_NumFrame, m_AlignOption, m_AV, m_CanRetrieveSeq, m_cur_align, m_currAlignHsp, m_currAlignSeqListIndex, m_MasterGeneticCode, m_NumAlignToShow, m_QueryNumber, m_Scope, m_SeqalignSetRef, m_SlaveGeneticCode, CSeq_id::Match(), NCBI_THROW, CObjectOStream::Open(), out(), s_GetStdsegMasterFrame(), CAlnVec::SetAaCoding(), CAlnVec::SetGenCode(), CException::what(), x_DisplayAlnvec(), x_DisplayAlnvecInfo(), x_GetAlnVecForSeqalign(), x_InitAlignParams(), and x_PreProcessSeqAlign().

Referenced by BOOST_AUTO_TEST_CASE(), TestUtil::PrintFormattedSeqAlign(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), TestSimpleAlignment(), and CBlastFormat::x_DisplayAlignsWithTemplates().

◆ operator=()

CDisplaySeqalign& CDisplaySeqalign::operator= ( const CDisplaySeqalign rhs)
private

Prohibit assignment operator.

◆ PrepareBlastUngappedSeqalign()

CRef< CSeq_align_set > CDisplaySeqalign::PrepareBlastUngappedSeqalign ( const objects::CSeq_align_set &  alnset)
static

static functions Need to call this if the seqalign is stdseg or dendiag for ungapped blast alignment display as each stdseg ro dendiag is a distinct alignment.

Don't call it for other case as it's a waste of time.

Parameters
alnsetinput alnset
Returns
processed alnset

Definition at line 3164 of file showalign.cpp.

References CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Std, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetStd(), ITERATE, CSeq_align_set_Base::Set(), CSeq_align_Base::SetScore(), CSeq_align_Base::SetSegs(), CSeq_align_Base::SetType(), and CSeq_align_Base::C_Segs::Which().

Referenced by CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintReport(), s_SeqAlignToXMLHit(), CBlastFormat::x_PrintTabularReport(), and CBlastFormat::x_PrintTaxReport().

◆ PrepareBlastUngappedSeqalignEx()

CRef< CSeq_align_set > CDisplaySeqalign::PrepareBlastUngappedSeqalignEx ( const objects::CSeq_align_set &  alnset)
static

static functions same as PrepareBlastUngappedSeqalign, but process seg scores uniformly even if there is only a single seg.

Parameters
alnsetinput alnset
Returns
processed alnset

Definition at line 3218 of file showalign.cpp.

References CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Std, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetStd(), ITERATE, CSeq_align_set_Base::Set(), CSeq_align_Base::SetScore(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::C_Segs::Which().

◆ PrepareBlastUngappedSeqalignEx2()

CRef< CSeq_align_set > CDisplaySeqalign::PrepareBlastUngappedSeqalignEx2 ( objects::CSeq_align_set &  alnset)
static

◆ SetAlignOption()

void CDisplaySeqalign::SetAlignOption ( int  option)
inline

Set functions.

Set according to DsiplayOption

Parameters
optiondisplay option disired

Definition at line 283 of file showalign.hpp.

References m_AlignOption, and option.

Referenced by BOOST_AUTO_TEST_CASE(), TestUtil::PrintFormattedSeqAlign(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), TestSimpleAlignment(), and CBlastFormat::x_SetAlignParameters().

◆ SetAlignSeqListIndex()

void CDisplaySeqalign::SetAlignSeqListIndex ( int  alignSeqListIndex)
inline

Set subject seq index.

Parameters
alignSeqListIndexsubject seq index in descriptions table

Definition at line 401 of file showalign.hpp.

References m_currAlignSeqListIndex.

◆ SetAlignTemplates()

void CDisplaySeqalign::SetAlignTemplates ( SAlignTemplates alignTemplates)
inline

Definition at line 452 of file showalign.hpp.

References m_AlignTemplates.

Referenced by CBlastFormat::x_DisplayAlignsWithTemplates().

◆ SetAlignType()

void CDisplaySeqalign::SetAlignType ( AlignType  type)
inline

Needed only if you want to display positives and strand.

Parameters
typetype of seqalign

Definition at line 346 of file showalign.hpp.

References m_AlignType, and type.

Referenced by CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), and CBlastFormat::x_SetAlignParameters().

◆ SetBlastType()

void CDisplaySeqalign::SetBlastType ( string  type)
inline

internal blast type

Parameters
typerefer to blobj->adm->trace->created_by

Definition at line 395 of file showalign.hpp.

References m_BlastType, and type.

◆ SetCddRid()

void CDisplaySeqalign::SetCddRid ( string  cdd_rid)
inline

CDD rid for constructing linkout.

Parameters
cdd_ridcdd RID

Definition at line 374 of file showalign.hpp.

References m_CddRid.

◆ SetCgiContext()

void CDisplaySeqalign::SetCgiContext ( CCgiContext ctx)
inline

Definition at line 409 of file showalign.hpp.

References ctx, and m_Ctx.

◆ SetDbName()

void CDisplaySeqalign::SetDbName ( string  name)
inline

set blast database name

Parameters
namedb name

Definition at line 353 of file showalign.hpp.

References m_DbName.

Referenced by BOOST_AUTO_TEST_CASE(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), TestSimpleAlignment(), and CBlastFormat::x_SetAlignParameters().

◆ SetDbType()

void CDisplaySeqalign::SetDbType ( bool  is_na)
inline

database type.

used for seq fetching from blast db

Parameters
is_nais nuc database or not

Definition at line 360 of file showalign.hpp.

References m_IsDbNa.

Referenced by BOOST_AUTO_TEST_CASE(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), TestSimpleAlignment(), and CBlastFormat::x_SetAlignParameters().

◆ SetEntrezTerm()

void CDisplaySeqalign::SetEntrezTerm ( string  term)
inline

for constructing structure linkout

Parameters
termentrez query term

Definition at line 381 of file showalign.hpp.

References m_EntrezTerm.

◆ SetLineLen()

void CDisplaySeqalign::SetLineLen ( size_t  len)
inline

number of bases or amino acids per line

Parameters
lenlength desired

Definition at line 305 of file showalign.hpp.

References len, and m_LineLen.

Referenced by CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), and CBlastFormat::x_SetAlignParameters().

◆ SetLinkoutDB()

void CDisplaySeqalign::SetLinkoutDB ( ILinkoutDB l,
const string mv_build_name 
)
inline

Set the linkout implementation.

Definition at line 249 of file showalign.hpp.

References m_LinkoutDB, and m_MapViewerBuildName.

◆ SetMasterDomain()

void CDisplaySeqalign::SetMasterDomain ( list< CRef< DomainInfo > > *  domain)
inline

Definition at line 455 of file showalign.hpp.

References m_DomainInfo.

Referenced by CBlastFormat::PrintOneResultSet().

◆ SetMasterGeneticCode()

void CDisplaySeqalign::SetMasterGeneticCode ( int  code)
inline

Set genetic code for master sequence.

Parameters
codethe genetic code

Definition at line 330 of file showalign.hpp.

References m_MasterGeneticCode.

Referenced by CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), and CBlastFormat::x_SetAlignParameters().

◆ SetMiddleLineStyle()

void CDisplaySeqalign::SetMiddleLineStyle ( MiddleLineStyle  option = eBar)
inline

set middle line style

Parameters
optionstyle desired

Definition at line 323 of file showalign.hpp.

References m_MidLineStyle, and option.

Referenced by CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), and CBlastFormat::x_SetAlignParameters().

◆ SetNumAlignToShow()

void CDisplaySeqalign::SetNumAlignToShow ( int  num)
inline

Display top num seqalign Note this only limit the number of seqalign regardless of the seqids.

This won't work if you want to limit the number of hits (or nmuber of database seqeunces) as in blast display.

Parameters
numnumber desired

Definition at line 316 of file showalign.hpp.

References m_NumAlignToShow.

Referenced by CBlastFormat::PrintOneResultSet().

◆ SetPreComputedResID()

void CDisplaySeqalign::SetPreComputedResID ( string  preComputedResID)
inline

Sets CDD precomputed results ID.

Parameters
stringcontaining seq id used in contsructing URL to CDART

Definition at line 415 of file showalign.hpp.

References m_PreComputedResID.

◆ SetQueryAnchoredIndex()

void CDisplaySeqalign::SetQueryAnchoredIndex ( int  queryAnchoredSetIndex)
inline

Sets index of Query anchored alignment set to display or download.

Index corresponds to cosequent query ranges For example range 1-60 - m_QueryAnchoredSetIndex=1, range 61-120 m_QueryAnchoredSetIndex=2

Parameters
intqueryAnchoredSetIndex

Definition at line 425 of file showalign.hpp.

References m_QueryAnchoredSetIndex.

◆ SetQueryNumber()

void CDisplaySeqalign::SetQueryNumber ( int  number)
inline

for linking to mapviewer

Parameters
numberblast query number

Definition at line 388 of file showalign.hpp.

References m_QueryNumber, and number.

Referenced by CBlastFormat::x_SetAlignParameters().

◆ SetResultPositionIndex()

void CDisplaySeqalign::SetResultPositionIndex ( int  index)
inline

Definition at line 466 of file showalign.hpp.

References m_ResultPositionIndex.

Referenced by CBlastFormat::PrintOneResultSet().

◆ SetRid()

void CDisplaySeqalign::SetRid ( string  rid)
inline

set blast request id

Parameters
ridblast RID

Definition at line 367 of file showalign.hpp.

References m_Rid.

◆ SetSeqLocChar()

void CDisplaySeqalign::SetSeqLocChar ( SeqLocCharOption  option = eX)
inline

character style for seqloc display such as masked region

Parameters
optioncharacter style option

Definition at line 291 of file showalign.hpp.

References m_SeqLocChar, and option.

Referenced by BOOST_AUTO_TEST_CASE(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), TestSimpleAlignment(), and CBlastFormat::x_SetAlignParameters().

◆ SetSeqLocColor()

void CDisplaySeqalign::SetSeqLocColor ( SeqLocColorOption  option = eBlack)
inline

color for seqloc display such as masked region

Parameters
optioncolor desired

Definition at line 298 of file showalign.hpp.

References m_SeqLocColor, and option.

Referenced by CBlastFormat::x_SetAlignParameters().

◆ SetSequencePropertyLabel()

void CDisplaySeqalign::SetSequencePropertyLabel ( const vector< string > *  SequencePropertyLabel,
EOwnership  ownership = eNoOwnership 
)
inline

Definition at line 460 of file showalign.hpp.

References m_SeqPropertyLabel, and AutoPtr< X, Del >::reset().

Referenced by CBlastFormat::PrintOneResultSet().

◆ SetSlaveGeneticCode()

void CDisplaySeqalign::SetSlaveGeneticCode ( int  code)
inline

Set Genetic cod for slaves.

Parameters
codethe genetic code

Definition at line 337 of file showalign.hpp.

References m_SlaveGeneticCode.

Referenced by CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), and CBlastFormat::x_SetAlignParameters().

◆ SetSubjectMasks()

void CDisplaySeqalign::SetSubjectMasks ( const TSeqLocInfoVector masks)

Sets the masks and the masking algorithm used for the subject sequences.

Parameters
maskssubject masks [in]

Definition at line 1052 of file showalign.cpp.

References ITERATE, and m_SubjectMasks.

Referenced by CBlastFormat::PrintOneResultSet().

◆ SetTranslatedFrameForLocalSeq()

void CDisplaySeqalign::SetTranslatedFrameForLocalSeq ( TranslatedFrameForLocalSeq  frame)
inline

Definition at line 191 of file showalign.hpp.

References m_TranslatedFrameForLocalSeq.

Referenced by CBlastFormat::PrintOneResultSet().

◆ UseLongSequenceIds()

void CDisplaySeqalign::UseLongSequenceIds ( void  )
inline

Sets usage of long sequence ids (database|accession)

Definition at line 420 of file showalign.hpp.

References m_UseLongSeqIds.

Referenced by CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), and TestSimpleAlignment().

◆ x_AddTranslationForLocalSeq()

void CDisplaySeqalign::x_AddTranslationForLocalSeq ( vector< TSAlnFeatureInfoList > &  retval,
vector< string > &  sequence 
) const
protected

◆ x_CalcUrlLinksParams()

void CDisplaySeqalign::x_CalcUrlLinksParams ( const objects::CSeq_align &  align,
string  idString,
string  toolUrl 
)
protected

◆ x_DisplayAlignInfo()

void CDisplaySeqalign::x_DisplayAlignInfo ( CNcbiOstream out,
SAlnInfo aln_vec_info 
)
protected

◆ x_DisplayAlignSortInfo()

void CDisplaySeqalign::x_DisplayAlignSortInfo ( CNcbiOstream out,
string  id_label 
)
protected

◆ x_DisplayAlnvec()

void CDisplaySeqalign::x_DisplayAlnvec ( CNcbiOstream out)
protected

Display the current alnvec.

Parameters
outstream for display

Definition at line 1814 of file showalign.cpp.

References out(), x_DisplayRowData(), and x_PrepareRowData().

Referenced by DisplaySeqalign().

◆ x_DisplayAlnvecInfo()

void CDisplaySeqalign::x_DisplayAlnvecInfo ( CNcbiOstream out,
SAlnInfo aln_vec_info,
bool  show_defline 
)
protected

◆ x_DisplayAlnvecInfoHead()

void CDisplaySeqalign::x_DisplayAlnvecInfoHead ( CNcbiOstream out,
SAlnInfo aln_vec_info 
)
protected

◆ x_DisplayBl2SeqLink()

void CDisplaySeqalign::x_DisplayBl2SeqLink ( CNcbiOstream out)
protected

◆ x_DisplayIdentityInfo()

void CDisplaySeqalign::x_DisplayIdentityInfo ( SAlnRowInfo alnRoInfo,
CNcbiOstream out 
)
protected

Display identities,positives,frames etc.

◆ x_DisplayInsertsForQueryAnchored()

void CDisplaySeqalign::x_DisplayInsertsForQueryAnchored ( SAlnRowInfo alnRoInfo,
int  row,
CNcbiOstrstream out 
)
protected

◆ x_DisplayMiddLine()

void CDisplaySeqalign::x_DisplayMiddLine ( SAlnRowInfo alnRoInfo,
int  row,
CNcbiOstrstream out 
)
protected

◆ x_DisplayMpvAnchor()

void CDisplaySeqalign::x_DisplayMpvAnchor ( CNcbiOstream out,
SAlnInfo aln_vec_info 
)
protected

Display anchor for links from mapview.

Definition at line 3465 of file showalign.cpp.

References buffer, CSeq_id::eContent, eHtml, m_AlignOption, m_AV, m_BlastType, max(), min(), out(), NStr::ToLower(), and NStr::TruncateSpaces().

Referenced by x_ShowAlnvecInfo(), and x_ShowAlnvecInfoTemplate().

◆ x_DisplayRowData() [1/2]

string CDisplaySeqalign::x_DisplayRowData ( SAlnRowInfo alnRoInfo)
protectedvirtual

◆ x_DisplayRowData() [2/2]

void CDisplaySeqalign::x_DisplayRowData ( SAlnRowInfo alnRoInfo,
CNcbiOstream out 
)
protectedvirtual

◆ x_DisplayRowDataSet()

string CDisplaySeqalign::x_DisplayRowDataSet ( SAlnRowInfo alnRoInfo,
int  aln_start,
vector< int > &  prev_stop 
)
protected

◆ x_DisplaySequenceIDForPairwise()

void CDisplaySeqalign::x_DisplaySequenceIDForPairwise ( SAlnRowInfo alnRoInfo,
int  row,
bool  has_mismatch,
CNcbiOstrstream out 
)
protected

◆ x_DisplaySequenceIDForQueryAnchored()

void CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored ( SAlnRowInfo alnRoInfo,
int  row,
CNcbiOstrstream out 
)
protected

◆ x_DisplaySequenceLine()

void CDisplaySeqalign::x_DisplaySequenceLine ( SAlnRowInfo alnRoInfo,
int  row,
int  prev_stop,
CNcbiOstrstream out 
)
protected

◆ x_DisplaySingleAlignParams()

void CDisplaySeqalign::x_DisplaySingleAlignParams ( CNcbiOstream out,
SAlnInfo aln_vec_info,
bool  showSortControls 
)
protected

◆ x_DoFills()

void CDisplaySeqalign::x_DoFills ( int  row,
objects::CAlnMap::TSignedRange &  aln_range,
int  aln_start,
TSInsertInformationList insert_list,
list< string > &  inserts 
) const
protected

recusively fill the insert for anchored view

Parameters
rowthe row number
aln_rangethe alignment range
aln_startstart for current row
insert_listinformation containing the insert info
insertsinserts strings to be inserted

Definition at line 3035 of file showalign.cpp.

References COpenRange< Position >::GetLength(), m_AV, NON_CONST_ITERATE, row, s_AdjustInsert(), and x_AddBar().

Referenced by x_FillInserts().

◆ x_FillAlnDispParams() [1/2]

SAlnDispParams* CDisplaySeqalign::x_FillAlnDispParams ( const CRef< objects::CBlast_def_line > &  iter,
const objects::CBioseq_Handle &  bsp_handle,
list< string > &  use_this_seqid,
TGi  firstGi,
int  numLinkoutReads 
)
protected

◆ x_FillAlnDispParams() [2/2]

SAlnDispParams* CDisplaySeqalign::x_FillAlnDispParams ( const objects::CBioseq_Handle &  bsp_handle)
protected

◆ x_FillIdentityInfo()

void CDisplaySeqalign::x_FillIdentityInfo ( const string sequence_standard,
const string sequence,
int match,
int positive,
string middle_line 
)
protected

compute number of identical and positive residues and set middle line accordingly

Parameters
sequence_standardthe master sequence
sequencethe slave sequence
matchthe number of identical match
positivenumber of positive match
middle_linethe middle line to be filled

Definition at line 2124 of file showalign.cpp.

References eBar, eChar, eProt, eShowMiddleLine, i, m_AlignOption, m_AlignType, m_Matrix, m_MidLineStyle, match(), and positive().

Referenced by x_PrepareIdentityInfo().

◆ x_FillInserts()

void CDisplaySeqalign::x_FillInserts ( int  row,
objects::CAlnMap::TSignedRange &  aln_range,
int  aln_start,
list< string > &  inserts,
string insert_pos_string,
TSInsertInformationList insert_list 
) const
protected

get inserts info

Parameters
rowcurrent row
aln_rangethe alignment range
aln_startstart for current row
insertsinserts to be filled
insert_pos_stringstring to indicate the start of insert
insert_listinformation containing the insert info

Definition at line 3083 of file showalign.cpp.

References COpenRange< Position >::GetLength(), ITERATE, row, and x_DoFills().

Referenced by x_DisplayInsertsForQueryAnchored().

◆ x_FillLocList()

void CDisplaySeqalign::x_FillLocList ( TSAlnSeqlocInfoList loc_list,
const list< CRef< CSeqLocInfo > > *  masks 
) const
protected

convert the passed seqloc list info using alnment coordinates

Parameters
loc_listfill the list with seqloc info using aln coordinates
masksthe masked regions

Definition at line 4282 of file showalign.cpp.

References IAlnExplorer::eBackwards, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_interval_Base::GetTo(), i, ITERATE, m_AV, and CSeq_id::Match().

Referenced by x_PrepareRowData().

◆ x_FillSeqid()

void CDisplaySeqalign::x_FillSeqid ( string id,
int  row 
) const
protected

◆ x_FormatAlignSortInfo()

string CDisplaySeqalign::x_FormatAlignSortInfo ( )
protected

◆ x_FormatAlnBlastInfo()

string CDisplaySeqalign::x_FormatAlnBlastInfo ( SAlnInfo aln_vec_info)
protected

◆ x_FormatAlnHSPLinks()

string CDisplaySeqalign::x_FormatAlnHSPLinks ( string alignInfo)
protected

◆ x_FormatDefLinesHeader()

string CDisplaySeqalign::x_FormatDefLinesHeader ( const objects::CBioseq_Handle &  bsp_handle,
SAlnInfo aln_vec_info 
)
protected

◆ x_FormatDynamicFeaturesInfo()

string CDisplaySeqalign::x_FormatDynamicFeaturesInfo ( string  alignInfo,
SAlnInfo aln_vec_info 
)
protected

◆ x_FormatIdentityInfo()

string CDisplaySeqalign::x_FormatIdentityInfo ( string  alignInfo,
SAlnInfo aln_vec_info 
)
protected

◆ x_FormatOneDynamicFeature()

string CDisplaySeqalign::x_FormatOneDynamicFeature ( string  viewerURL,
TGi  subjectGi,
int  fromRange,
int  toRange,
string  featText 
)
protected

◆ x_FormatSingleAlign()

string CDisplaySeqalign::x_FormatSingleAlign ( SAlnInfo aln_vec_info)
protected

◆ x_GetAlnVecForSeqalign()

CRef< CAlnVec > CDisplaySeqalign::x_GetAlnVecForSeqalign ( const objects::CSeq_align &  align)
protected

◆ x_GetDomainInfo()

void CDisplaySeqalign::x_GetDomainInfo ( int  row_num,
int  aln_stop,
vector< TSAlnFeatureInfoList > &  retval 
) const
protected

Definition at line 4417 of file showalign.cpp.

References m_AV, m_DomainInfo, max(), min(), s_MakeDomainString(), and x_SetFeatureInfo().

Referenced by x_PrepareRowData().

◆ x_GetDumpgnlLink()

string CDisplaySeqalign::x_GetDumpgnlLink ( const list< CRef< objects::CSeq_id > > &  ids) const
protected

get dumpgnl url to sequence record

Parameters
idsid list
rowthe current row
alternative_urluser specified url or empty string
taxidtaxid

Definition at line 3144 of file showalign.cpp.

References CAlignFormatUtil::BuildUserUrl(), FindBestChoice(), CAlignFormatUtil::GetLabel(), kDownloadImg, kDownloadLink, kDownloadUrl, label, m_DbName, m_IsDbNa, m_QueryNumber, m_Rid, CAlignFormatUtil::MapTemplate(), NcbiEmptyString, CSeq_id::WorstRank(), x_GetSegs(), and ZERO_TAX_ID.

◆ x_GetFeatureInfo()

void CDisplaySeqalign::x_GetFeatureInfo ( TSAlnFeatureInfoList feature,
int  custom_genetic_code,
objects::CScope &  scope,
objects::CSeqFeatData::E_Choice  choice,
int  row,
string sequence,
list< list< CRange< TSeqPos > > > &  feat_seq_range,
list< objects::ENa_strand > &  feat_seq_strand,
bool  fill_feat_range 
) const
protected

get feature info

Parameters
featurewhere feature info to be filled
custom_genetic_codeuse this code (set to -1 if you don't want to use this code)
scopescope to fectch sequence
choicewhich feature to get
rowcurrent row number
sequencethe sequence string
feat_seq_rangeto be filled with the feature seqlocs of this row
feat_seq_strandstrand to be filled corresponding to feat_seq_range
fill_feat_rangeto fill feat_seq_range?

Definition at line 2620 of file showalign.cpp.

References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, COpenRange< Position >::Empty(), eNa_strand_minus, eNa_strand_plus, fFGL_Both, FindGi(), CScope::GetBioseqHandle(), CRange_Base::GetFrom(), GetLabel(), CRange_Base::GetTo(), CSeq_loc::GetTotalRange(), i, isalpha(), IsSameBioseq(), ITERATE, k_FeatureIdLen, k_IntronChar, m_AV, m_LineLen, m_SlaveGeneticCode, max(), min(), NcbiEmptyString, CRef< C, Locker >::Reset(), row, s_FillCdsStartPosition(), s_GetCdsSequence(), s_GetConcatenatedExon(), s_MapSlaveFeatureToMaster(), SAnnotSelector::SetAdaptiveDepth(), SAnnotSelector::SetResolveAll(), x_SetFeatureInfo(), and ZERO_GI.

Referenced by x_PrepareRowData().

◆ x_GetGeneLinkUrl()

string CDisplaySeqalign::x_GetGeneLinkUrl ( int  gene_id)
protected

get the URL of the Gene info link.

Parameters
gene_idgene id to link to.
Returns
: fully formatted URL of the Gene info link.

Definition at line 3333 of file showalign.cpp.

References buf, CAlignFormatUtil::GetURLFromRegistry(), m_cur_align, m_IsDbNa, and m_Rid.

◆ x_GetGiForSeqIdList()

static TGi CDisplaySeqalign::x_GetGiForSeqIdList ( const list< CRef< objects::CSeq_id > > &  ids)
staticprotected

◆ x_GetInserts()

void CDisplaySeqalign::x_GetInserts ( TSInsertInformationList insert_list,
objects::CAlnMap::TSeqPosList &  insert_aln_start,
objects::CAlnMap::TSeqPosList &  insert_seq_start,
objects::CAlnMap::TSeqPosList &  insert_length,
int  line_aln_stop 
)
protected

get insert information

Parameters
insert_listlist to be filled
insert_aln_startalnment start coordinate info
insert_seq_startalnment sequence start info
insert_lengthinsert length info
line_aln_stopalignment stop for this row

Definition at line 3103 of file showalign.cpp.

Referenced by x_DisplayInsertsForQueryAnchored().

◆ x_GetLinkout()

int CDisplaySeqalign::x_GetLinkout ( const objects::CSeq_id &  id)
protected

◆ x_GetNumGaps()

int CDisplaySeqalign::x_GetNumGaps ( )
protected

Count number of total gaps.

Returns
: number of toal gaps for the current alnvec

Definition at line 2580 of file showalign.cpp.

References CSeq_align_Base::eType_global, i, m_AV, m_SeqalignSetRef, and row.

Referenced by x_PrepareIdentityInfo().

◆ x_GetQueryFeatureList()

void CDisplaySeqalign::x_GetQueryFeatureList ( int  row_num,
int  aln_stop,
vector< TSAlnFeatureInfoList > &  features 
) const
protected

get external query feature info such as phi blast pattern

Parameters
row_numrow number
aln_stopthe stop position for the whole alignment
featuresthe return value for this method

Definition at line 4331 of file showalign.cpp.

References i, m_AV, m_QueryFeature, NcbiEmptyString, and x_SetFeatureInfo().

Referenced by x_PrepareRowData().

◆ x_GetSegs()

string CDisplaySeqalign::x_GetSegs ( int  row) const
protected

segments starts and stops used for map viewer, etc

Parameters
rowrow number
Returns
: the seg string

Definition at line 3126 of file showalign.cpp.

References eMergeAlign, NStr::IntToString(), m_AlignOption, m_AlnLinksParams, m_AV, NcbiEmptyString, and row.

Referenced by x_GetDumpgnlLink(), and x_InitAlignLinks().

◆ x_HTMLSeqIDLink()

string CDisplaySeqalign::x_HTMLSeqIDLink ( SAlnRowInfo alnRoInfo,
int  row,
TGi  giToUse 
)
protected

◆ x_InitAlignLinks()

void CDisplaySeqalign::x_InitAlignLinks ( SAlnDispParams alnDispParams,
const list< CRef< objects::CBlast_def_line > > &  bdl_list,
int  lnkDispPrarms 
)
protected

◆ x_InitAlignParams()

void CDisplaySeqalign::x_InitAlignParams ( objects::CSeq_align_set &  actual_aln_list)
protected

◆ x_InitDefLinesHeader()

string CDisplaySeqalign::x_InitDefLinesHeader ( const objects::CBioseq_Handle &  bsp_handle,
SAlnInfo aln_vec_info 
)
protected

◆ x_InitSeqUrl()

CAlignFormatUtil::SSeqURLInfo * CDisplaySeqalign::x_InitSeqUrl ( TGi  giToUse,
string  accession,
TTaxId  taxid,
const list< CRef< objects::CSeq_id > > &  ids 
)
protected

◆ x_MapDefLine()

string CDisplaySeqalign::x_MapDefLine ( SAlnDispParams alnDispParams,
bool  isFisrt,
bool  linkout,
bool  hideDefline,
int  seqLength 
)
protected

◆ x_OutputSeq()

void CDisplaySeqalign::x_OutputSeq ( string sequence,
const objects::CSeq_id &  id,
int  start,
int  len,
int  frame,
int  row,
bool  color_mismatch,
const TSAlnSeqlocInfoList loc_list,
CNcbiOstream out 
) const
protected

display sequence for one row

Parameters
sequencethe sequence for that row
idseqid
startseqalign coodinate
lenlength desired
framefor tranlated alignment
rowthe current row
color_mismatchcolorize the mismatch or not
loc_listseqlocs to be shown as specified in constructor
outoutput stream

Definition at line 2489 of file showalign.cpp.

References _ASSERT, color, CSeq_id_Base::e_not_set, eColorDifferentBases, eHtml, eLowerCase, eN, eShowIdentity, eX, CRange_Base::GetFrom(), CRange_Base::GetTo(), i, int, isalpha(), ITERATE, k_DefaultMaskSeqLocTempl, k_IdentityChar, len, m_AlignOption, m_SeqLocChar, m_SeqLocColor, CAlignFormatUtil::MapTemplate(), out(), s_ColorDifferentBases(), s_ProcessStyledContent(), COpenRange< Position >::Set(), and tolower().

Referenced by x_DisplayMiddLine(), and x_DisplaySequenceLine().

◆ x_PrepareDynamicFeatureInfo()

void CDisplaySeqalign::x_PrepareDynamicFeatureInfo ( SAlnInfo aln_vec_info)
protected

◆ x_PrepareIdentityInfo()

void CDisplaySeqalign::x_PrepareIdentityInfo ( SAlnInfo aln_vec_info)
protected

◆ x_PrepareRowData()

CDisplaySeqalign::SAlnRowInfo * CDisplaySeqalign::x_PrepareRowData ( void  )
protected

Calculate data for pairwise alignment display.

Definition at line 1205 of file showalign.cpp.

References _ASSERT, CDisplaySeqalign::SAlnRowInfo::align_length, CDisplaySeqalign::SAlnRowInfo::align_stats, CDisplaySeqalign::SAlnRowInfo::bioseqFeature, CDisplaySeqalign::SAlnRowInfo::colorMismatch, NStr::DoubleToString(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeq_id_Base::e_Local, eHtml, eMasterAnchored, eMergeAlign, eNa_strand_minus, eNa_strand_plus, eProt, eShowAlignStatsForMultiAlignView, eShowCdsFeature, eShowEndGaps, eShowGeneFeature, eShowSequencePropertyLabel, eShowTranslationForLocalSeq, FindGi(), CDisplaySeqalign::SAlnRowInfo::frame, GetId(), CAlignFormatUtil::GetTaxidForSeqid(), i, CDisplaySeqalign::SAlnRowInfo::insertAlnStart, CDisplaySeqalign::SAlnRowInfo::insertLength, CDisplaySeqalign::SAlnRowInfo::insertStart, NStr::IntToString(), ITERATE, m_AlignOption, m_AlignTemplates, m_AlignType, m_AV, m_BlastType, m_DomainInfo, m_featScope, m_LineLen, m_Scope, m_Seqloc, m_SeqPropertyLabel, m_SubjectMasks, CDisplaySeqalign::SAlnRowInfo::masked_regions, CDisplaySeqalign::SAlnRowInfo::match, match(), max(), CDisplaySeqalign::SAlnRowInfo::max_align_stats_len, CDisplaySeqalign::SAlnRowInfo::max_feature_num, CDisplaySeqalign::SAlnRowInfo::max_seq_property_label, CDisplaySeqalign::SAlnRowInfo::maxIdLen, CDisplaySeqalign::SAlnRowInfo::maxStartLen, CDisplaySeqalign::SAlnRowInfo::middleLine, NcbiEmptyString, NON_CONST_ITERATE, NULL, CDisplaySeqalign::SAlnRowInfo::percent_ident, row, CDisplaySeqalign::SAlnRowInfo::rowNum, CDisplaySeqalign::SAlnRowInfo::rowRng, s_CalculateIdentity(), s_GetFrame(), s_MakeNewMasterSeq(), CDisplaySeqalign::SAlnRowInfo::seq_property_label, CDisplaySeqalign::SAlnRowInfo::seqidArray, CDisplaySeqalign::SAlnRowInfo::seqStarts, CDisplaySeqalign::SAlnRowInfo::seqStops, CDisplaySeqalign::SAlnRowInfo::sequence, ncbi::grid::netcache::search::fields::size, NStr::SizetToString(), CDisplaySeqalign::SAlnRowInfo::taxid, NStr::ToLower(), NStr::TruncateSpaces(), x_AddTranslationForLocalSeq(), x_FillLocList(), x_FillSeqid(), x_GetDomainInfo(), x_GetFeatureInfo(), x_GetQueryFeatureList(), ZERO_GI, and ZERO_TAX_ID.

Referenced by x_DisplayAlnvec(), and x_DisplayAlnvecInfo().

◆ x_PreProcessSeqAlign()

void CDisplaySeqalign::x_PreProcessSeqAlign ( objects::CSeq_align_set &  actual_aln_list)
protected

Sets m_Segs,m_HspNumber.

Definition at line 4567 of file showalign.cpp.

Referenced by DisplaySeqalign().

◆ x_PreProcessSingleAlign()

void CDisplaySeqalign::x_PreProcessSingleAlign ( objects::CSeq_align_set::Tdata::const_iterator  currSeqAlignIter,
objects::CSeq_align_set &  actual_aln_list,
bool  multipleSeqs 
)
protected

Definition at line 4650 of file showalign.cpp.

References IRegistry::Get(), m_BlastType, and m_Reg.

◆ x_PrintDefLine()

string CDisplaySeqalign::x_PrintDefLine ( const objects::CBioseq_Handle &  bsp_handle,
SAlnInfo aln_vec_info 
)
protected

◆ x_PrintDynamicFeatures() [1/2]

void CDisplaySeqalign::x_PrintDynamicFeatures ( CNcbiOstream out,
SAlnInfo aln_vec_info 
)
protected

output dynamic feature url

Parameters
outoutput stream

Definition at line 4210 of file showalign.cpp.

References eHtml, CAlignFormatUtil::GetURLFromRegistry(), ITERATE, m_AlignOption, m_IsDbNa, m_Rid, NStr::NumericToString(), out(), s_MapFeatureURL(), and ZERO_GI.

◆ x_PrintDynamicFeatures() [2/2]

string CDisplaySeqalign::x_PrintDynamicFeatures ( void  )
protected

◆ x_PrintFeatures()

void CDisplaySeqalign::x_PrintFeatures ( SAlnRowInfo alnRoInfo,
int  row,
string master_feat_str,
CNcbiOstream out 
)
protected

◆ x_ProcessRowDataSet()

void CDisplaySeqalign::x_ProcessRowDataSet ( SAlnRowInfo alnRoInfo,
int  aln_start,
vector< int > &  prev_stop 
)
protected

◆ x_SetFeatureInfo()

void CDisplaySeqalign::x_SetFeatureInfo ( CRef< SAlnFeatureInfo feat_info,
const objects::CSeq_loc &  seqloc,
int  aln_from,
int  aln_to,
int  aln_stop,
char  pattern_char,
string  pattern_id,
string alternative_feat_str,
int  genetic_code 
) const
protected

set feature info

Parameters
feat_infofeature to fill in
seqlocfeature for this seqloc
aln_fromfrom coodinate
aln_toto coordinate
aln_stopthe stop position for whole alignment
pattern_charthe pattern character to show
pattern_idthe pattern id to show
alternative_feat_struse this as feature string instead

Definition at line 2950 of file showalign.cpp.

References NcbiEmptyString.

Referenced by x_AddTranslationForLocalSeq(), x_GetDomainInfo(), x_GetFeatureInfo(), and x_GetQueryFeatureList().

◆ x_ShowAlnvecInfo()

void CDisplaySeqalign::x_ShowAlnvecInfo ( CNcbiOstream out,
SAlnInfo aln_vec_info,
bool  show_defline 
)
protected

◆ x_ShowAlnvecInfoTemplate()

void CDisplaySeqalign::x_ShowAlnvecInfoTemplate ( CNcbiOstream out,
SAlnInfo aln_vec_info,
bool  show_defline 
)
protected

Member Data Documentation

◆ m_AlignedRegionsUrl

string CDisplaySeqalign::m_AlignedRegionsUrl
protected

Definition at line 642 of file showalign.hpp.

Referenced by x_InitAlignLinks().

◆ m_AlignOption

int CDisplaySeqalign::m_AlignOption
protected

◆ m_AlignTemplates

SAlignTemplates* CDisplaySeqalign::m_AlignTemplates
protected

◆ m_AlignType

AlignType CDisplaySeqalign::m_AlignType
protected

◆ m_AlnLinksParams

map< string, struct SAlnLinksParams > CDisplaySeqalign::m_AlnLinksParams
protected

Definition at line 637 of file showalign.hpp.

Referenced by x_DisplaySingleAlignParams(), x_GetSegs(), x_InitSeqUrl(), and x_MapDefLine().

◆ m_AV

objects::CAlnVec* CDisplaySeqalign::m_AV
protected

◆ m_BlastType

string CDisplaySeqalign::m_BlastType
protected

◆ m_CanRetrieveSeq

bool CDisplaySeqalign::m_CanRetrieveSeq
protected

◆ m_CddRid

string CDisplaySeqalign::m_CddRid
protected

Definition at line 630 of file showalign.hpp.

Referenced by SetCddRid(), and x_InitAlignParams().

◆ m_ConfigFile

CNcbiIfstream* CDisplaySeqalign::m_ConfigFile
protected

Definition at line 633 of file showalign.hpp.

Referenced by x_InitAlignParams(), and ~CDisplaySeqalign().

◆ m_Ctx

CCgiContext* CDisplaySeqalign::m_Ctx
protected

◆ m_cur_align

int CDisplaySeqalign::m_cur_align
mutableprotected

Gene info reader object, reads Gene info entries from files.

Current alignment index (added to the linkout and entrez URL's)

Definition at line 656 of file showalign.hpp.

Referenced by DisplaySeqalign(), x_DisplaySequenceIDForQueryAnchored(), x_FormatDefLinesHeader(), x_GetGeneLinkUrl(), x_InitAlignLinks(), x_InitDefLinesHeader(), x_InitSeqUrl(), and x_PrintDefLine().

◆ m_currAlignHsp

int CDisplaySeqalign::m_currAlignHsp
protected

Current HSP number for single alignmnet.

Definition at line 660 of file showalign.hpp.

Referenced by DisplaySeqalign(), x_FormatAlnBlastInfo(), x_FormatSingleAlign(), and x_ShowAlnvecInfoTemplate().

◆ m_currAlignSeqListIndex

int CDisplaySeqalign::m_currAlignSeqListIndex
protected

Current subject seq index in descriptions table.

Definition at line 662 of file showalign.hpp.

Referenced by DisplaySeqalign(), and SetAlignSeqListIndex().

◆ m_CurrAlnAccession

string CDisplaySeqalign::m_CurrAlnAccession
protected

◆ m_CurrAlnID_DbLbl

string CDisplaySeqalign::m_CurrAlnID_DbLbl
protected

gi(if exists) that is used for html formatting otherwise id with db part like ti:xxxxxxx or GNOMON:XXXXXX

Definition at line 676 of file showalign.hpp.

Referenced by x_FormatAlignSortInfo(), x_FormatDefLinesHeader(), and x_InitDefLinesHeader().

◆ m_CurrAlnID_Lbl

string CDisplaySeqalign::m_CurrAlnID_Lbl
protected

gi(if exists) that is used for html formatting otherwise id without db part

Definition at line 672 of file showalign.hpp.

Referenced by x_FormatAlignSortInfo(), x_FormatAlnBlastInfo(), x_FormatDefLinesHeader(), x_FormatSingleAlign(), and x_InitDefLinesHeader().

◆ m_CustomLinksList

list<string> CDisplaySeqalign::m_CustomLinksList
protected

Definition at line 638 of file showalign.hpp.

Referenced by x_FormatDefLinesHeader(), and x_InitAlignLinks().

◆ m_DbName

string CDisplaySeqalign::m_DbName
protected

Definition at line 626 of file showalign.hpp.

Referenced by SetDbName(), x_GetDumpgnlLink(), x_InitAlignParams(), and x_InitSeqUrl().

◆ m_DomainInfo

list<CRef<DomainInfo> >* CDisplaySeqalign::m_DomainInfo
protected

Definition at line 611 of file showalign.hpp.

Referenced by SetMasterDomain(), x_GetDomainInfo(), and x_PrepareRowData().

◆ m_DynamicFeature

objects::CGetFeature* CDisplaySeqalign::m_DynamicFeature
protected

◆ m_EntrezTerm

string CDisplaySeqalign::m_EntrezTerm
protected

Definition at line 631 of file showalign.hpp.

Referenced by SetEntrezTerm(), and x_InitAlignParams().

◆ m_FASTAlinkUrl

string CDisplaySeqalign::m_FASTAlinkUrl
protected

Definition at line 641 of file showalign.hpp.

Referenced by x_InitAlignLinks().

◆ m_FeatObj

CRef< objects::CObjectManager > CDisplaySeqalign::m_FeatObj
protected

Definition at line 646 of file showalign.hpp.

Referenced by x_InitAlignParams().

◆ m_featScope

CRef< objects::CScope > CDisplaySeqalign::m_featScope
protected

Definition at line 647 of file showalign.hpp.

Referenced by x_InitAlignParams(), and x_PrepareRowData().

◆ m_HSPLinksList

list<string> CDisplaySeqalign::m_HSPLinksList
protected

Definition at line 640 of file showalign.hpp.

Referenced by x_FormatAlnHSPLinks(), and x_InitAlignLinks().

◆ m_IsDbNa

bool CDisplaySeqalign::m_IsDbNa
protected

◆ m_LineLen

size_t CDisplaySeqalign::m_LineLen
protected

◆ m_LinkoutDB

ILinkoutDB* CDisplaySeqalign::m_LinkoutDB
protected

Reference to LinkoutDB implementation. Not owned by this class.

Definition at line 667 of file showalign.hpp.

Referenced by SetLinkoutDB(), x_GetLinkout(), and x_InitAlignParams().

◆ m_LinkoutInfo

CAlignFormatUtil::SLinkoutInfo CDisplaySeqalign::m_LinkoutInfo
protected

Definition at line 643 of file showalign.hpp.

Referenced by x_InitAlignLinks(), and x_InitAlignParams().

◆ m_LinkoutList

list<string> CDisplaySeqalign::m_LinkoutList
protected

Definition at line 639 of file showalign.hpp.

Referenced by x_FormatDefLinesHeader(), and x_InitAlignLinks().

◆ m_LinkoutOrder

string CDisplaySeqalign::m_LinkoutOrder
protected

Definition at line 628 of file showalign.hpp.

Referenced by x_InitAlignParams().

◆ m_MapViewerBuildName

string CDisplaySeqalign::m_MapViewerBuildName
protected

mapviewer build name associated with the sequences in the BLAST database out of which the results are being formatted by this class.

Definition at line 670 of file showalign.hpp.

Referenced by SetLinkoutDB(), x_GetLinkout(), and x_InitAlignParams().

◆ m_MasterGeneticCode

int CDisplaySeqalign::m_MasterGeneticCode
protected

Definition at line 649 of file showalign.hpp.

Referenced by DisplaySeqalign(), and SetMasterGeneticCode().

◆ m_Matrix

int** CDisplaySeqalign::m_Matrix
protected

Definition at line 616 of file showalign.hpp.

Referenced by x_FillIdentityInfo(), and ~CDisplaySeqalign().

◆ m_MidLineStyle

MiddleLineStyle CDisplaySeqalign::m_MidLineStyle
protected

Definition at line 648 of file showalign.hpp.

Referenced by SetMiddleLineStyle(), and x_FillIdentityInfo().

◆ m_NumAlignToShow

int CDisplaySeqalign::m_NumAlignToShow
protected

Definition at line 620 of file showalign.hpp.

Referenced by DisplaySeqalign(), and SetNumAlignToShow().

◆ m_NumBlastDefLines

int CDisplaySeqalign::m_NumBlastDefLines
protected

Number of subject sequence deflines.

Definition at line 658 of file showalign.hpp.

Referenced by x_FormatDefLinesHeader(), and x_InitDefLinesHeader().

◆ m_PreComputedResID

string CDisplaySeqalign::m_PreComputedResID
protected

CDD precomputed results ID.

Definition at line 664 of file showalign.hpp.

Referenced by SetPreComputedResID(), and x_InitAlignParams().

◆ m_QueryAnchoredSetIndex

int CDisplaySeqalign::m_QueryAnchoredSetIndex
protected

Definition at line 687 of file showalign.hpp.

Referenced by SetQueryAnchoredIndex(), and x_DisplayRowData().

◆ m_QueryFeature

list< FeatureInfo * >* CDisplaySeqalign::m_QueryFeature
protected

external feature such as phiblast

Definition at line 610 of file showalign.hpp.

Referenced by x_GetQueryFeatureList().

◆ m_QueryNumber

int CDisplaySeqalign::m_QueryNumber
protected

◆ m_Reg

CNcbiRegistry* CDisplaySeqalign::m_Reg
protected

◆ m_ResultPositionIndex

int CDisplaySeqalign::m_ResultPositionIndex
protected

result position index for multiple query case

Definition at line 683 of file showalign.hpp.

Referenced by SetResultPositionIndex(), and x_DisplaySequenceIDForQueryAnchored().

◆ m_Rid

string CDisplaySeqalign::m_Rid
protected

◆ m_Scope

objects::CScope& CDisplaySeqalign::m_Scope
protected

◆ m_SeqalignSetRef

CConstRef< objects::CSeq_align_set > CDisplaySeqalign::m_SeqalignSetRef
protected

reference to seqalign set

Definition at line 604 of file showalign.hpp.

Referenced by DisplaySeqalign(), x_DisplayAlignInfo(), x_FormatAlnBlastInfo(), and x_GetNumGaps().

◆ m_Seqloc

list< CRef<CSeqLocInfo> >* CDisplaySeqalign::m_Seqloc
protected

display character option for list of seqloc

Definition at line 607 of file showalign.hpp.

Referenced by x_PrepareRowData().

◆ m_SeqLocChar

SeqLocCharOption CDisplaySeqalign::m_SeqLocChar
protected

Definition at line 621 of file showalign.hpp.

Referenced by SetSeqLocChar(), and x_OutputSeq().

◆ m_SeqLocColor

SeqLocColorOption CDisplaySeqalign::m_SeqLocColor
protected

Definition at line 622 of file showalign.hpp.

Referenced by SetSeqLocColor(), and x_OutputSeq().

◆ m_SeqPropertyLabel

AutoPtr<const vector<string> > CDisplaySeqalign::m_SeqPropertyLabel
protected

Definition at line 612 of file showalign.hpp.

Referenced by SetSequencePropertyLabel(), and x_PrepareRowData().

◆ m_SlaveGeneticCode

int CDisplaySeqalign::m_SlaveGeneticCode
protected

Definition at line 650 of file showalign.hpp.

Referenced by DisplaySeqalign(), SetSlaveGeneticCode(), and x_GetFeatureInfo().

◆ m_SubjectMasks

TSubjectMaskMap CDisplaySeqalign::m_SubjectMasks
protected

Map of subject masks.

Definition at line 601 of file showalign.hpp.

Referenced by SetSubjectMasks(), and x_PrepareRowData().

◆ m_TotalHSPNum

int CDisplaySeqalign::m_TotalHSPNum
protected

◆ m_TranslatedFrameForLocalSeq

TranslatedFrameForLocalSeq CDisplaySeqalign::m_TranslatedFrameForLocalSeq
protected

Definition at line 680 of file showalign.hpp.

Referenced by SetTranslatedFrameForLocalSeq(), and x_AddTranslationForLocalSeq().

◆ m_UseLongSeqIds

bool CDisplaySeqalign::m_UseLongSeqIds
protected

print long sequence ids (with gi and accession with database source)

Definition at line 686 of file showalign.hpp.

Referenced by UseLongSequenceIds(), x_InitDefLinesHeader(), x_MapDefLine(), and x_PrintDefLine().


The documentation for this class was generated from the following files:
Modified on Fri Jul 19 17:07:27 2024 by modify_doxy.py rev. 669887