Search Toolkit Book for CDisplaySeqalign

#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, TMaskedQueryRegions >	TSubjectMaskMap
	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::SSeqURLInfo *	x_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...

SAlnRowInfo *	x_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)

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

SAlnDispParams *	x_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

CNcbiIfstream *	m_ConfigFile

CNcbiRegistry *	m_Reg

objects::CGetFeature *	m_DynamicFeature

map< string, struct SAlnLinksParams >	m_AlnLinksParams

list< string >	m_CustomLinksList

list< string >	m_LinkoutList

list< string >	m_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

CCgiContext *	m_Ctx

SAlignTemplates *	m_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...

ILinkoutDB *	m_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...

CDisplaySeqalign &	operator= (const CDisplaySeqalign &rhs)
	Prohibit assignment operator. More...

Detailed Description

Definition at line 91 of file showalign.hpp.

Member Typedef Documentation

◆ TSAlnFeatureInfoList

typedef list< CRef<SAlnFeatureInfo> > CDisplaySeqalign::TSAlnFeatureInfoList

protected

Definition at line 496 of file showalign.hpp.

◆ TSAlnSeqlocInfoList

typedef list< CRef<SAlnSeqlocInfo> > CDisplaySeqalign::TSAlnSeqlocInfoList

protected

List of SAlnSeqlocInfo structures.

Definition at line 505 of file showalign.hpp.

◆ TSInsertInformationList

typedef list< CRef<SInsertInformation> > CDisplaySeqalign::TSInsertInformationList

protected

Definition at line 486 of file showalign.hpp.

◆ TSubjectMaskMap

typedef map< SSeqIdKey, TMaskedQueryRegions > CDisplaySeqalign::TSubjectMaskMap

protected

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

Definition at line 598 of file showalign.hpp.

Member Enumeration Documentation

◆ AlignType

enum CDisplaySeqalign::AlignType

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

Enumerator
eNotSet
eNuc
eProt

Definition at line 98 of file showalign.hpp.

◆ DisplayOption

enum CDisplaySeqalign::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

enum CDisplaySeqalign::LinksDisplayParams

Enumerator
eDisplayDefault
eDisplayResourcesLinks
eDisplayDownloadLink

Definition at line 219 of file showalign.hpp.

◆ MiddleLineStyle

enum CDisplaySeqalign::MiddleLineStyle

Middle line style option.

Enumerator
eChar
eBar

Definition at line 196 of file showalign.hpp.

◆ SeqLocCharOption

enum CDisplaySeqalign::SeqLocCharOption

character used to display seqloc, such as masked sequence

Enumerator
eX
eN
eLowerCase

Definition at line 203 of file showalign.hpp.

◆ SeqLocColorOption

enum CDisplaySeqalign::SeqLocColorOption

colors for seqloc display

Enumerator
eBlack
eGrey
eRed

Definition at line 212 of file showalign.hpp.

◆ TranslatedFrameForLocalSeq

enum CDisplaySeqalign::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

seqalign	seqalign to display.
mask_seqloc	seqloc to be displayed with different characters and colors such as masked sequence.
external_feature	Feature to display such as phiblast pattern. Must be seqloc-int
matrix_name	scoring matrix name [in]
scope	scope to fetch your sequence

◆ ~CDisplaySeqalign()

CDisplaySeqalign::~CDisplaySeqalign ( )

virtual

Destructor.

Definition at line 221 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 4675 of file showalign.cpp.

◆ DisplaySeqalign()

void CDisplaySeqalign::DisplaySeqalign ( CNcbiOstream & out )

call this to display seqalign

Parameters

out	stream for display

Definition at line 1910 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

alnset input alnset

Returns: processed alnset

Definition at line 3159 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

alnset input alnset

Returns: processed alnset

Definition at line 3213 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

same as PrepareBlastUngappedSeqalign2, but sets aggregate scores.

Parameters

alnset input alnset

Returns: processed alnset

Definition at line 3249 of file showalign.cpp.

References CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Std, CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetStd(), ITERATE, CObject_id::Match(), NON_CONST_ITERATE, CSeq_align_set_Base::Set(), CObject_id_Base::SetId(), CSeq_align_Base::SetScore(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::C_Segs::Which().

◆ SetAlignOption()

void CDisplaySeqalign::SetAlignOption ( int option )

inline

Set functions.

Set according to DsiplayOption

Parameters

option display 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

alignSeqListIndex subject 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

type	type 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

type	refer 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_rid cdd 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

name db 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_na is 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

term	entrez 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

len	length 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 l(), 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

code	the 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

option style 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

num	number 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

string containing 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

int	queryAnchoredSetIndex

Definition at line 425 of file showalign.hpp.

References m_QueryAnchoredSetIndex.

◆ SetQueryNumber()

void CDisplaySeqalign::SetQueryNumber ( int number )

inline

for linking to mapviewer

Parameters

number blast 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

rid blast 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

option character 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

option color 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

code	the 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

masks subject masks [in]

Definition at line 1047 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

Definition at line 1080 of file showalign.cpp.

References eExtreme_Biological, i, int, m_AV, m_Scope, m_TranslatedFrameForLocalSeq, s_GetFinalTranslatedString(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), ncbi::grid::netcache::search::fields::size, CSeqTranslator::Translate(), and x_SetFeatureInfo().

Referenced by x_PrepareRowData().

◆ x_CalcUrlLinksParams()

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

protected

Definition at line 4601 of file showalign.cpp.

References first(), CAlnMap::GetSeqStart(), CAlnMap::GetSeqStop(), and NStr::IntToString().

◆ x_DisplayAlignInfo()

void CDisplaySeqalign::x_DisplayAlignInfo	(	CNcbiOstream &	out,
		SAlnInfo *	aln_vec_info
	)

protected

Display score,bits,expect,method.

Definition at line 3565 of file showalign.cpp.

References CDisplaySeqalign::SAlnInfo::bits, CDisplaySeqalign::SAlnInfo::comp_adj_method, eShowRawScoreOnly, CSeq_align_Base::eType_global, CDisplaySeqalign::SAlnInfo::evalue, CAlignFormatUtil::GetScoreString(), m_AlignOption, m_SeqalignSetRef, out(), CDisplaySeqalign::SAlnInfo::score, and CDisplaySeqalign::SAlnInfo::sum_n.

Referenced by x_DisplaySingleAlignParams().

◆ x_DisplayAlignSortInfo()

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

protected

Display Sorting controls.

Definition at line 3345 of file showalign.cpp.

References CAlignFormatUtil::AddSpace(), CAlignFormatUtil::BuildFormatQueryString(), CAlignFormatUtil::eEvalue, CAlignFormatUtil::eHspPercentIdentity, CAlignFormatUtil::eQueryStart, CAlignFormatUtil::eScore, CAlignFormatUtil::eSubjectStart, CCgiContext::GetRequestValue(), CCgiEntry::GetValue(), map_checker< Container >::insert(), m_Ctx, NcbiEmptyString, out(), and NStr::StringToInt().

Referenced by x_DisplaySingleAlignParams().

◆ x_DisplayAlnvec()

void CDisplaySeqalign::x_DisplayAlnvec ( CNcbiOstream & out )

protected

Display the current alnvec.

Parameters

out	stream for display

Definition at line 1809 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

display alnvec info

Parameters

out	output stream
aln_vec_info	alnvec list

Definition at line 3941 of file showalign.cpp.

References CDisplaySeqalign::SAlnInfo::alnRowInfo, CDisplaySeqalign::SAlnInfo::alnvec, eShowBlastInfo, eShowMiddleLine, m_AlignOption, m_AlignTemplates, m_AV, out(), x_PrepareDynamicFeatureInfo(), x_PrepareIdentityInfo(), x_PrepareRowData(), x_ShowAlnvecInfo(), and x_ShowAlnvecInfoTemplate().

Referenced by DisplaySeqalign().

◆ x_DisplayAlnvecInfoHead()

void CDisplaySeqalign::x_DisplayAlnvecInfoHead	(	CNcbiOstream &	out,
		SAlnInfo *	aln_vec_info
	)

protected

◆ x_DisplayBl2SeqLink()

void CDisplaySeqalign::x_DisplayBl2SeqLink ( CNcbiOstream & out )

protected

Dipslay Bl2seq TBLASTX link.

Definition at line 3444 of file showalign.cpp.

References eGetId_Best, FindGi(), CBioseq_Handle::GetBioseqCore(), GetId(), CBioseq_Base::GetId(), GI_TO, kBl2seqUrl, m_AV, CAlignFormatUtil::MapTemplate(), and out().

Referenced by x_ShowAlnvecInfo(), and x_ShowAlnvecInfoTemplate().

◆ 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

Definition at line 1629 of file showalign.cpp.

Referenced by x_DisplayRowDataSet().

◆ x_DisplayMiddLine()

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

protected

Definition at line 1776 of file showalign.cpp.

References CAlignFormatUtil::AddSpace(), CDisplaySeqalign::SAlnRowInfo::currActualLineLen, CDisplaySeqalign::SAlnRowInfo::currPrintSegment, k_IdStartMargin, k_StartSequenceMargin, CDisplaySeqalign::SAlnRowInfo::masked_regions, CDisplaySeqalign::SAlnRowInfo::maxIdLen, CDisplaySeqalign::SAlnRowInfo::maxStartLen, CDisplaySeqalign::SAlnRowInfo::middleLine, out(), row, and x_OutputSeq().

Referenced by x_DisplayRowDataSet().

◆ x_DisplayMpvAnchor()

void CDisplaySeqalign::x_DisplayMpvAnchor	(	CNcbiOstream &	out,
		SAlnInfo *	aln_vec_info
	)

protected

Display anchor for links from mapview.

Definition at line 3460 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

Display pairwise alignment.

Definition at line 1409 of file showalign.cpp.

References eMergeAlign, eShowAlignStatsForMultiAlignView, eShowSequencePropertyLabel, int, m_AlignOption, m_AV, m_LineLen, out(), CDisplaySeqalign::SAlnRowInfo::rowNum, CDisplaySeqalign::SAlnRowInfo::show_align_stats, CDisplaySeqalign::SAlnRowInfo::show_seq_property_label, and x_DisplayRowDataSet().

Referenced by x_DisplayAlnvec(), x_FormatSingleAlign(), and x_ShowAlnvecInfo().

◆ 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

Definition at line 1476 of file showalign.cpp.

Referenced by x_DisplayRowData().

◆ x_DisplaySequenceIDForPairwise()

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

protected

Definition at line 1679 of file showalign.cpp.

References eColorDifferentBases, eHtml, eMergeAlign, eShowIdentity, k_DefaultPairwiseWithIdntTempl, m_AlignOption, CAlignFormatUtil::MapTemplate(), out(), row, and CDisplaySeqalign::SAlnRowInfo::seqidArray.

Referenced by x_DisplayRowDataSet().

◆ x_DisplaySequenceIDForQueryAnchored()

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

protected

Definition at line 1694 of file showalign.cpp.

References CAlignFormatUtil::AddSpace(), CDisplaySeqalign::SAlnRowInfo::align_stats, CSeq_id_Base::e_Gi, CSeq_id::eContent, eHtml, eHyperLinkMasterSeqid, eHyperLinkSlaveSeqid, eMergeAlign, eSequenceRetrieval, eShowCheckBox, FindBestChoice(), CAlignFormatUtil::GetGiForSeqIdList(), GetId(), CAlignFormatUtil::GetLabel(), NStr::IntToString(), CSeq_id_Base::IsLocal(), k_AlignStatsMargin, k_DefaultAnchorTempl, k_DefaultAnchorWithPosTempl, k_DefaultCheckboxExTempl, k_DefaultCheckboxTempl, k_DefaultSpaceMaintainerTempl, k_SequencePropertyLabelMargin, m_AlignOption, m_AV, m_CanRetrieveSeq, m_cur_align, m_QueryNumber, m_ResultPositionIndex, CAlignFormatUtil::MapTemplate(), CDisplaySeqalign::SAlnRowInfo::max_align_stats_len, CDisplaySeqalign::SAlnRowInfo::max_seq_property_label, NcbiEmptyString, NStr::NumericToString(), out(), row, CDisplaySeqalign::SAlnRowInfo::seq_property_label, CDisplaySeqalign::SAlnRowInfo::seqidArray, CDisplaySeqalign::SAlnRowInfo::show_align_stats, CDisplaySeqalign::SAlnRowInfo::show_seq_property_label, CSeq_id::WorstRank(), x_HTMLSeqIDLink(), and ZERO_GI.

Referenced by x_DisplayRowDataSet().

◆ 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

Display Sorting controls,score,bits,expect,method,features identities,positives,frames etc.

Definition at line 3970 of file showalign.cpp.

Referenced by x_ShowAlnvecInfo().

◆ 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

row	the row number
aln_range	the alignment range
aln_start	start for current row
insert_list	information containing the insert info
inserts	inserts strings to be inserted

Definition at line 3030 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

Referenced by x_InitDefLinesHeader(), and x_PrintDefLine().

◆ 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_standard	the master sequence
sequence	the slave sequence
match	the number of identical match
positive	number of positive match
middle_line	the middle line to be filled

Definition at line 2119 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

row	current row
aln_range	the alignment range
aln_start	start for current row
inserts	inserts to be filled
insert_pos_string	string to indicate the start of insert
insert_list	information containing the insert info

Definition at line 3078 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_list	fill the list with seqloc info using aln coordinates
masks	the masked regions

Definition at line 4277 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

make the appropriate seqid

Parameters

id	the id to be filled
row	row number

Definition at line 4480 of file showalign.cpp.

References CSeq_id_Base::e_Gi, CSeq_id::eContent, eMergeAlign, eShowBlastStyleId, eShowGi, FindBestChoice(), CAlignFormatUtil::GetGiForSeqIdList(), CAlignFormatUtil::GetLabel(), kQuery, kSubject(), m_AlignOption, m_AV, NStr::NumericToString(), row, CSeq_id::WorstRank(), and ZERO_GI.

Referenced by x_PrepareRowData().

◆ x_FormatAlignSortInfo()

string CDisplaySeqalign::x_FormatAlignSortInfo ( )

protected

Definition at line 3425 of file showalign.cpp.

References CCgiContext::GetRequestValue(), CCgiEntry::GetValue(), i, NStr::IntToString(), kEmptyStr, m_AlignTemplates, m_Ctx, m_CurrAlnID_DbLbl, m_CurrAlnID_Lbl, CAlignFormatUtil::MapTemplate(), NcbiEmptyString, CDisplaySeqalign::SAlignTemplates::sortInfoTmpl, and NStr::StringToInt().

Referenced by x_FormatDefLinesHeader().

◆ x_FormatAlnBlastInfo()

string CDisplaySeqalign::x_FormatAlnBlastInfo ( SAlnInfo * aln_vec_info )

protected

Definition at line 3490 of file showalign.cpp.

References CDisplaySeqalign::SAlignTemplates::alignInfoMethodTmpl, CDisplaySeqalign::SAlignTemplates::alignInfoTmpl, CSeq_align_Base::eType_global, CAlignFormatUtil::GetScoreString(), NStr::IntToString(), m_AlignTemplates, m_AV, m_currAlignHsp, m_CurrAlnAccession, m_CurrAlnID_Lbl, m_SeqalignSetRef, m_TotalHSPNum, CAlignFormatUtil::MapTemplate(), and compile_time_bits::range().

Referenced by x_FormatSingleAlign().

◆ x_FormatAlnHSPLinks()

string CDisplaySeqalign::x_FormatAlnHSPLinks ( string & alignInfo )

protected

Definition at line 4011 of file showalign.cpp.

References int, ITERATE, m_AV, m_CurrAlnAccession, m_HSPLinksList, CAlignFormatUtil::MapTemplate(), max(), and compile_time_bits::range().

Referenced by x_FormatSingleAlign().

◆ 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

Definition at line 4149 of file showalign.cpp.

References CAlignFormatUtil::GetURLFromRegistry(), NStr::IntToString(), ITERATE, CAlignFormatUtil::MapTemplate(), and x_FormatOneDynamicFeature().

Referenced by x_FormatSingleAlign().

◆ x_FormatIdentityInfo()

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

protected

Definition at line 244 of file showalign.cpp.

References CDisplaySeqalign::SAlignTemplates::alignInfoFrameTmpl, CDisplaySeqalign::SAlnInfo::alnRowInfo, eProt, CDisplaySeqalign::SAlnRowInfo::frame, CDisplaySeqalign::SAlnInfo::gap, CDisplaySeqalign::SAlnInfo::identity, int, NStr::IntToString(), m_AlignTemplates, m_AlignType, m_AV, CAlignFormatUtil::MapTemplate(), CDisplaySeqalign::SAlnInfo::match, and CDisplaySeqalign::SAlnInfo::positive.

Referenced by x_FormatSingleAlign().

◆ x_FormatOneDynamicFeature()

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

protected

Definition at line 4120 of file showalign.cpp.

References CDisplaySeqalign::SAlignTemplates::alignFeatureLinkTmpl, CDisplaySeqalign::SAlignTemplates::alignFeatureTmpl, m_AlignTemplates, m_CurrAlnAccession, m_IsDbNa, m_Rid, CAlignFormatUtil::MapTemplate(), s_MapFeatureURL(), and ZERO_GI.

Referenced by x_FormatDynamicFeaturesInfo().

◆ x_FormatSingleAlign()

string CDisplaySeqalign::x_FormatSingleAlign ( SAlnInfo * aln_vec_info )

protected

Definition at line 4045 of file showalign.cpp.

References CDisplaySeqalign::SAlignTemplates::alignInfoTmpl, CDisplaySeqalign::SAlignTemplates::alignRowTmpl, CDisplaySeqalign::SAlignTemplates::alignRowTmplLast, eShowBlastInfo, NStr::IntToString(), m_AlignOption, m_AlignTemplates, m_currAlignHsp, m_CurrAlnID_Lbl, m_TotalHSPNum, CAlignFormatUtil::MapTemplate(), x_DisplayRowData(), x_FormatAlnBlastInfo(), x_FormatAlnHSPLinks(), x_FormatDynamicFeaturesInfo(), and x_FormatIdentityInfo().

Referenced by x_ShowAlnvecInfoTemplate().

◆ 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 4412 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

ids	id list
row	the current row
alternative_url	user specified url or empty string
taxid	taxid

Definition at line 3139 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

feature	where feature info to be filled
custom_genetic_code	use this code (set to -1 if you don't want to use this code)
scope	scope to fectch sequence
choice	which feature to get
row	current row number
sequence	the sequence string
feat_seq_range	to be filled with the feature seqlocs of this row
feat_seq_strand	strand to be filled corresponding to feat_seq_range
fill_feat_range	to fill feat_seq_range?

Definition at line 2615 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_id gene id to link to.

Returns: : fully formatted URL of the Gene info link.

Definition at line 3328 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_list	list to be filled
insert_aln_start	alnment start coordinate info
insert_seq_start	alnment sequence start info
insert_length	insert length info
line_aln_stop	alignment stop for this row

Definition at line 3098 of file showalign.cpp.

Referenced by x_DisplayInsertsForQueryAnchored().

◆ x_GetLinkout()

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

protected

Definition at line 2159 of file showalign.cpp.

References eLinkout, ERR_POST, ILinkoutDB::GetLinkout(), CException::GetMsg(), m_AlignOption, m_LinkoutDB, and m_MapViewerBuildName.

◆ x_GetNumGaps()

int CDisplaySeqalign::x_GetNumGaps ( )

protected

Count number of total gaps.

Returns: : number of toal gaps for the current alnvec

Definition at line 2575 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_num	row number
aln_stop	the stop position for the whole alignment
features	the return value for this method

Definition at line 4326 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

row	row number

Returns: : the seg string

Definition at line 3121 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

Definition at line 964 of file showalign.cpp.

References CAlignFormatUtil::SSeqURLInfo::defline, eShowInfoOnMouseOverSeqid, CBioseq_Handle::GetBioseqCore(), CAlignFormatUtil::GetFullIDLink(), CBioseq_Base::GetId(), m_AlignOption, m_AV, NcbiEmptyString, row, CDisplaySeqalign::SAlnRowInfo::seqidArray, CDisplaySeqalign::SAlnRowInfo::taxid, CAlignFormatUtil::SSeqURLInfo::useTemplates, and x_InitSeqUrl().

Referenced by x_DisplaySequenceIDForQueryAnchored().

◆ x_InitAlignLinks()

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

protected

Definition at line 1006 of file showalign.cpp.

Referenced by x_InitDefLinesHeader().

◆ x_InitAlignParams()

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

protected

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.

Definition at line 1869 of file showalign.cpp.

References CSeq_id::eContent, CAlignFormatUtil::eDbTypeNotSet, eDynamicFeature, eHtml, eLinkout, eMasterAnchored, eShowCdsFeature, eShowGeneFeature, false, FindBestChoice(), IRegistry::Get(), CSeq_align_set_Base::Get(), CAlignFormatUtil::GetDbType(), CObjectManager::GetInstance(), CSeq_id::GetLabel(), CGBDataLoader::GetLoaderNameFromArgs(), CAlignFormatUtil::SLinkoutInfo::Init(), kLinkoutOrderStr, m_AlignOption, m_BlastType, m_CanRetrieveSeq, m_CddRid, m_ConfigFile, m_DbName, m_DynamicFeature, m_EntrezTerm, m_FeatObj, m_featScope, m_IsDbNa, m_LinkoutDB, m_LinkoutInfo, m_LinkoutOrder, m_MapViewerBuildName, m_PreComputedResID, m_QueryNumber, m_Reg, m_Rid, m_Scope, NcbiEmptyString, CAlignFormatUtil::SLinkoutInfo::queryID, CGBDataLoader::RegisterInObjectManager(), and CSeq_id::WorstRank().

Referenced by DisplaySeqalign().

◆ x_InitDefLinesHeader()

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

protected

Definition at line 3708 of file showalign.cpp.

References CDisplaySeqalign::SAlignTemplates::alnTitlesLinkTmpl, CDisplaySeqalign::SAlignTemplates::alnTitlesTmpl, CSeq_id::eContent, eDisplayDownloadLink, eDisplayResourcesLinks, eHtml, eLinkout, CRef< C, Locker >::Empty(), env, CSeqDB::ExtractBlastDefline(), CBlast_def_line_set_Base::Get(), CAlignFormatUtil::GetBareId(), CBioseq_Handle::GetBioseqLength(), CAlignFormatUtil::GetDisplayIds(), CAlignFormatUtil::GetLabel(), CSeq_id::GetLabel(), CDisplaySeqalign::SAlnDispParams::gi, NStr::IntToString(), k_GetSubseqThreshhold, m_AlignOption, m_AlignTemplates, m_AV, m_cur_align, m_CurrAlnAccession, m_CurrAlnID_DbLbl, m_CurrAlnID_Lbl, m_NumBlastDefLines, m_Rid, m_UseLongSeqIds, CAlignFormatUtil::MapTemplate(), NULL, NStr::NumericToString(), CDisplaySeqalign::SAlnDispParams::seqID, NStr::Split(), CDisplaySeqalign::SAlnDispParams::title, x_FillAlnDispParams(), x_InitAlignLinks(), x_MapDefLine(), and ZERO_GI.

Referenced by x_FormatDefLinesHeader().

◆ x_InitSeqUrl()

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

protected

get url to sequence record

Parameters

ids	id list
seqUrlInfo	struct containging params for URL

Definition at line 979 of file showalign.cpp.

References CAlignFormatUtil::SSeqURLInfo::advancedView, eNewTargetWindow, eShowInfoOnMouseOverSeqid, IRegistry::Get(), CAlignFormatUtil::GetGiForSeqIdList(), m_AlignOption, m_AlignTemplates, m_AlnLinksParams, m_AV, m_BlastType, m_cur_align, m_DbName, m_IsDbNa, m_QueryNumber, m_Reg, m_Rid, NULL, compile_time_bits::range(), CAlignFormatUtil::SSeqURLInfo::resourcesUrl, CAlignFormatUtil::SSeqURLInfo::useTemplates, and ZERO_GI.

Referenced by x_HTMLSeqIDLink().

◆ 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

sequence	the sequence for that row
id	seqid
start	seqalign coodinate
len	length desired
frame	for tranlated alignment
row	the current row
color_mismatch	colorize the mismatch or not
loc_list	seqlocs to be shown as specified in constructor
out	output stream

Definition at line 2484 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

Calculate data for feature display.

Definition at line 4080 of file showalign.cpp.

References CSeq_id::eBoth, eDynamicFeature, FindBestChoice(), FindGi(), CBioseq_Handle::GetBioseqCore(), CBioseq_Base::GetId(), CSeq_id::GetLabel(), k_GetDynamicFeatureSeqLength, m_AlignOption, m_AV, m_DynamicFeature, NULL, compile_time_bits::range(), and CSeq_id::WorstRank().

Referenced by x_DisplayAlnvecInfo().

◆ x_PrepareIdentityInfo()

void CDisplaySeqalign::x_PrepareIdentityInfo ( SAlnInfo * aln_vec_info )

protected

Definition at line 1786 of file showalign.cpp.

References CDisplaySeqalign::SAlnInfo::alnRowInfo, CDisplaySeqalign::SAlnRowInfo::colorMismatch, eColorDifferentBases, eShowBlastInfo, CDisplaySeqalign::SAlnInfo::gap, CAlignFormatUtil::GetPercentMatch(), CDisplaySeqalign::SAlnInfo::identity, k_ColorMismatchIdentity, m_AlignOption, m_AV, CDisplaySeqalign::SAlnInfo::match, CDisplaySeqalign::SAlnRowInfo::middleLine, CDisplaySeqalign::SAlnInfo::positive, CDisplaySeqalign::SAlnRowInfo::sequence, x_FillIdentityInfo(), and x_GetNumGaps().

Referenced by x_DisplayAlnvecInfo().

◆ x_PrepareRowData()

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

protected

Calculate data for pairwise alignment display.

Definition at line 1200 of file showalign.cpp.

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 4562 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 4645 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

print defline

Parameters

bsp_handle	bioseq of interest
use_this_gi	display this gi instead

Returns: : string containig defline(s)

Definition at line 2278 of file showalign.cpp.

References buf, eHtml, eLinkout, CRef< C, Locker >::Empty(), env, eSequenceRetrieval, eShowGi, CSeqDB::ExtractBlastDefline(), FindBestChoice(), CBlast_def_line_set_Base::Get(), CAlignFormatUtil::GetBareId(), CBioseq_Handle::GetBioseqCore(), CBioseq_Base::GetId(), CHTMLHelper::HTMLEncode(), if(), NStr::IntToString(), k_DefaultCheckboxTempl, k_MaxDeflinesToShow, k_MinDeflinesToShow, m_AlignOption, m_CanRetrieveSeq, m_cur_align, m_QueryNumber, m_UseLongSeqIds, CAlignFormatUtil::MapTemplate(), NcbiEmptyString, NStr::NumericToString(), out(), s_WrapOutputLine(), util::strncmp(), CSeq_id::WorstRank(), x_FillAlnDispParams(), and ZERO_GI.

Referenced by x_ShowAlnvecInfo().

◆ x_PrintDynamicFeatures() [1/2]

void CDisplaySeqalign::x_PrintDynamicFeatures	(	CNcbiOstream &	out,
		SAlnInfo *	aln_vec_info
	)

protected

output dynamic feature url

Parameters

out	output stream

Definition at line 4205 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

Referenced by x_DisplaySingleAlignParams().

◆ x_PrintFeatures()

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

protected

print out features and fill master_feat_str if applicable

Parameters

feature	the feature info
row	row num
alignment_range	alignment range
aln_start	alignment start in align coordinates
line_length	length per line
id_length	the max seq id length
start_length	the max seq start postion string length
max_feature_num	max numbe of features contained
master_feat_str	the feature for master seq
out	the out stream

Definition at line 883 of file showalign.cpp.

Referenced by x_DisplayRowDataSet().

◆ x_ProcessRowDataSet()

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

protected

Definition at line 1556 of file showalign.cpp.

References CDisplaySeqalign::SAlnRowInfo::currActualLineLen, CDisplaySeqalign::SAlnRowInfo::currPrintSegment, CDisplaySeqalign::SAlnRowInfo::currRange, eShowGapOnlyLines, COpenRange< Position >::IntersectingWith(), m_AlignOption, m_AV, m_LineLen, NcbiEmptyString, row, CDisplaySeqalign::SAlnRowInfo::rowNum, CDisplaySeqalign::SAlnRowInfo::rowRng, CDisplaySeqalign::SAlnRowInfo::seqStarts, and CDisplaySeqalign::SAlnRowInfo::seqStops.

Referenced by x_DisplayRowData().

◆ 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_info	feature to fill in
seqloc	feature for this seqloc
aln_from	from coodinate
aln_to	to coordinate
aln_stop	the stop position for whole alignment
pattern_char	the pattern character to show
pattern_id	the pattern id to show
alternative_feat_str	use this as feature string instead