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NCBI C++ ToolKit: BLAST Formatting

static string CBlastFormatUtil::BlastGetVersion (const string program) Returns the version and release date, e.g. More...
static void CBlastFormatUtil::BlastPrintVersionInfo (const string program, bool html, CNcbiOstream &out) Print out blast engine version. More...
static void CBlastFormatUtil::BlastPrintReference (bool html, size_t line_len, CNcbiOstream &out, blast::CReference::EPublication publication=blast::CReference::eGappedBlast, bool is_psiblast=false) Print out blast reference. More...
static void CBlastFormatUtil::PrintDbInformation (size_t line_len, string definition_line, int nNumSeqs, Uint8 nTotalLength, bool html, bool with_links, CNcbiOstream &out) static void CBlastFormatUtil::PrintAsciiPssm (const objects::CPssmWithParameters &pssm, CConstRef< blast::CBlastAncillaryData > ancillary_data, CNcbiOstream &out) Prints the PSSM in ASCII format (as in blastpgp's -Q option) More...
static CRef< objects::CSeq_annot > CBlastFormatUtil::CreateSeqAnnotFromSeqAlignSet (const objects::CSeq_align_set &alnset, blast::EProgram program, const string &db_name, const string &db_title, bool vdb_search=false) static void CBlastFormatUtil::GetWholeAlnSeqStrings (string &query, string &subject, const objects::CDense_seg &ds, objects::CScope &scope, int master_gen_code, int slave_gen_code) static void CBlastFormatUtil::GetWholeAlnSeqStrings (string &query, string &masked_query, string &subject, const objects::CDense_seg &ds, objects::CScope &scope, int master_gen_code, int slave_gen_code, const ncbi::TMaskedQueryRegions &mask_info, align_format::CDisplaySeqalign::SeqLocCharOption mask_char, int query_frame) static void CBlastFormatUtil::InsertSubjectScores (objects::CSeq_align_set &org_align_set, const objects::CBioseq_Handle &query_handle, TSeqRange query_range=TSeqRange(), ESubjectScores score_type=eQueryCovPerSubj) CBlastFormattingMatrix::CBlastFormattingMatrix (int **data, unsigned int nrows, unsigned int ncols) Constructor - allocates the matrix with appropriate size and populates with the values retrieved from a scoring matrix, passed in as a 2-dimensional integer array. More...
SBlastXMLIncremental::SBlastXMLIncremental () Default ctor() More...
virtual IBlastXML2ReportData::~IBlastXML2ReportData () Our virtual destructor. More...
virtual string IBlastXML2ReportData::GetBlastProgramName (void) const =0 Returns BLAST program name as string. More...
virtual blast::EProgram IBlastXML2ReportData::GetBlastTask (void) const =0 Returns BLAST task as an enumerated value. More...
virtual string IBlastXML2ReportData::GetDatabaseName (void) const =0 Returns database name. More...
virtual double IBlastXML2ReportData::GetEvalueThreshold (void) const =0 Returns e-value theshold used in search. More...
virtual int IBlastXML2ReportData::GetGapOpeningCost (void) const =0 Returns gap opening cost used in search. More...
virtual int IBlastXML2ReportData::GetGapExtensionCost (void) const =0 Returns gap extension cost used in search. More...
virtual int IBlastXML2ReportData::GetMatchReward (void) const =0 Returns match reward, for blastn search only. More...
virtual int IBlastXML2ReportData::GetMismatchPenalty (void) const =0 Returns mismatch penalty, for blastn search only. More...
virtual string IBlastXML2ReportData::GetPHIPattern (void) const =0 Returns pattern string, for PHI BLAST search only. More...
virtual string IBlastXML2ReportData::GetFilterString (void) const =0 Returns filtering option string. More...
virtual string IBlastXML2ReportData::GetMatrixName (void) const =0 Returns matrix name. More...
virtual CBlastFormattingMatrix * IBlastXML2ReportData::GetMatrix (void) const =0 Returns a 256x256 ASCII-alphabet matrix, needed for formatting. More...
virtual CConstRef< objects::CSeq_loc > IBlastXML2ReportData::GetQuerySeqLoc (void) const =0 virtual const TMaskedQueryRegions & IBlastXML2ReportData::GetMaskLocations () const =0 Returns list of mask locations for a given query. More...
virtual Int8 IBlastXML2ReportData::GetDbNumSeqs (void) const =0 Returns number of database sequences. More...
virtual Int8 IBlastXML2ReportData::GetDbLength (void) const =0 Returns database length. More...
virtual int IBlastXML2ReportData::GetLengthAdjustment (int num) const =0 Returns length adjustment for a given query. More...
virtual Int8 IBlastXML2ReportData::GetEffectiveSearchSpace (int num) const =0 Returns effective search space for a given query. More...
virtual double IBlastXML2ReportData::GetLambda (int num) const =0 Returns Karlin-Altschul Lambda parameter for a given query. More...
virtual double IBlastXML2ReportData::GetKappa (int num) const =0 Returns Karlin-Altschul K parameter for a given query. More...
virtual double IBlastXML2ReportData::GetEntropy (int num) const =0 Returns Karlin-Altschul H parameter for a given query. More...
virtual CRef< objects::CScope > IBlastXML2ReportData::GetScope (void) const =0 Returns scope . More...
virtual CConstRef< objects::CSeq_align_set > IBlastXML2ReportData::GetAlignmentSet (int num) const =0 Returns a vector continaing set of alignments found for a given query. More...
virtual int IBlastXML2ReportData::GetQueryGeneticCode (void) const =0 master genetic code More...
virtual int IBlastXML2ReportData::GetDbGeneticCode (void) const =0 slave genetic code More...
virtual string IBlastXML2ReportData::GetMessages (int num) const =0 Get error messages. More...
virtual list< string > IBlastXML2ReportData::GetSubjectIds (void) const =0 virtual bool IBlastXML2ReportData::IsBl2seq (void) const =0 virtual int IBlastXML2ReportData::GetNumOfSearchResults (void) const =0 virtual bool IBlastXML2ReportData::CanGetTaxInfo (void) const =0 virtual bool IBlastXML2ReportData::IsGappedSearch (void) const =0 virtual int IBlastXML2ReportData::GetCompositionBasedStats (void) const =0 virtual string IBlastXML2ReportData::GetBl2seqMode (void) const =0 virtual bool IBlastXML2ReportData::IsIterativeSearch (void) const =0 virtual string IBlastXML2ReportData::GetEntrezQuery (void) const =0 void BlastXML2_FormatReport (const IBlastXML2ReportData *data, CNcbiOstream *out_stream) Fills all fields in the XML BLAST v2 output object. More...
void BlastXML2_FormatReport (const IBlastXML2ReportData *data, string file_name) void BlastXML2_PrintHeader (CNcbiOstream *out_stream) void BlastXML2_FormatError (int exit_code, string err_msg, CNcbiOstream *out_stream) void BlastJSON_FormatReport (const IBlastXML2ReportData *data, string file_name) void BlastJSON_FormatReport (const IBlastXML2ReportData *data, CNcbiOstream *out_stream) void BlastJSON_PrintHeader (CNcbiOstream *out_stream) virtual IBlastXMLReportData::~IBlastXMLReportData () Our virtual destructor. More...
virtual string IBlastXMLReportData::GetBlastProgramName (void) const =0 Returns BLAST program name as string. More...
virtual blast::EProgram IBlastXMLReportData::GetBlastTask (void) const =0 Returns BLAST task as an enumerated value. More...
virtual string IBlastXMLReportData::GetDatabaseName (void) const =0 Returns database name. More...
virtual double IBlastXMLReportData::GetEvalueThreshold (void) const =0 Returns e-value theshold used in search. More...
virtual int IBlastXMLReportData::GetGapOpeningCost (void) const =0 Returns gap opening cost used in search. More...
virtual int IBlastXMLReportData::GetGapExtensionCost (void) const =0 Returns gap extension cost used in search. More...
virtual int IBlastXMLReportData::GetMatchReward (void) const =0 Returns match reward, for blastn search only. More...
virtual int IBlastXMLReportData::GetMismatchPenalty (void) const =0 Returns mismatch penalty, for blastn search only. More...
virtual string IBlastXMLReportData::GetPHIPattern (void) const =0 Returns pattern string, for PHI BLAST search only. More...
virtual string IBlastXMLReportData::GetFilterString (void) const =0 Returns filtering option string. More...
virtual string IBlastXMLReportData::GetMatrixName (void) const =0 Returns matrix name. More...
virtual CBlastFormattingMatrix * IBlastXMLReportData::GetMatrix (void) const =0 Returns a 256x256 ASCII-alphabet matrix, needed for formatting. More...
virtual unsigned int IBlastXMLReportData::GetNumQueries (void) const =0 Returns number of query sequences. More...
virtual const TMaskedQueryRegions * IBlastXMLReportData::GetMaskLocations (int query_index) const =0 Returns list of mask locations for a given query. More...
virtual int IBlastXMLReportData::GetDbNumSeqs (void) const =0 Returns number of database sequences. More...
virtual Int8 IBlastXMLReportData::GetDbLength (void) const =0 Returns database length. More...
virtual int IBlastXMLReportData::GetLengthAdjustment (int query_index) const =0 Returns length adjustment for a given query. More...
virtual Int8 IBlastXMLReportData::GetEffectiveSearchSpace (int query_index) const =0 Returns effective search space for a given query. More...
virtual double IBlastXMLReportData::GetLambda (int query_index) const =0 Returns Karlin-Altschul Lambda parameter for a given query. More...
virtual double IBlastXMLReportData::GetKappa (int query_index) const =0 Returns Karlin-Altschul K parameter for a given query. More...
virtual double IBlastXMLReportData::GetEntropy (int query_index) const =0 Returns Karlin-Altschul H parameter for a given query. More...
virtual const objects::CSeq_loc * IBlastXMLReportData::GetQuery (int query_index) const =0 Returns a query Seq-loc for a given query index. More...
virtual objects::CScope * IBlastXMLReportData::GetScope (int query_index) const =0 Returns scope for a given query. More...
virtual const objects::CSeq_align_set * IBlastXMLReportData::GetAlignment (int query_index) const =0 Returns set of alignments found for a given query. More...
virtual bool IBlastXMLReportData::GetGappedMode (void) const =0 Returns true if search was gapped, false otherwise. More...
virtual int IBlastXMLReportData::GetMasterGeneticCode () const =0 master genetic code More...
virtual int IBlastXMLReportData::GetSlaveGeneticCode () const =0 slave genetic code More...
virtual vector< string > IBlastXMLReportData::GetMessages () const =0 Get error messages, one element per query (e.g. More...
void BlastXML_FormatReport (objects::CBlastOutput &bxmlout, const IBlastXMLReportData *data, CNcbiOstream *out_stream=NULL, SBlastXMLIncremental *incremental_struct=NULL) Fills all fields in the XML BLAST output object. More...
CBlastHitMatrix::CBlastHitMatrix (const list< CRef< CSeq_align > > &seqAligns, int height=600, int width=800, CImageIO::EType format=CImageIO::ePng, const string &font_path="") Constructor. More...
CBlastHitMatrix::~CBlastHitMatrix () Destructor. More...
void CBlastHitMatrix::SetFileName (string fileName) Inits file name if image is written to the file. More...
void CBlastHitMatrix::SetThumbnail (bool set) Indicates that thumbmail should be shown. More...
bool CBlastHitMatrix::IsFileOut (void) Checks if image is to be written to the file. More...
string CBlastHitMatrix::GetNetcacheID (void) Get netcache ID for the image stored in netcache. More...
string CBlastHitMatrix::GetErrorMessage (void) Get error message. More...
bool CBlastHitMatrix::Display (CNcbiOstream &out) Outputs the image into CNcbiOstream. More...
bool CBlastHitMatrix::WriteToFile (void) Outputs the image into the file (m_FileOut=true) or netcache. More...
void CBlastHitMatrix::x_InitObjectManager () Initializes Object Manager. More...
void CBlastHitMatrix::x_InitPort () Initializes CGlPane. More...
void CBlastHitMatrix::x_GetLabels (void) Creates Query and subject labels info. More...
bool CBlastHitMatrix::x_RenderImage (void) Renders a pairwise alignments between the first two Seq-id in the alignment. More...
void CBlastHitMatrix::x_PreProcess (void) Performs pre-processing for image rendering. More...
void CBlastHitMatrix::x_Render (void) Inits renderer display options and text labels. More...
void CBlastHitMatrix::x_InitGraphics (const string &font_path="") Initialize rendering environment. More...
◆ ESubjectScores Enumerator eNoQuerySubjCov eQueryCovPerSubj eQueryCovPerUniqSubj eBothQuerySubjCov

Definition at line 180 of file blastfmtutil.hpp.

◆ BlastGetVersion() ◆ BlastJSON_FormatReport() [1/2] ◆ BlastJSON_FormatReport() [2/2] ◆ BlastJSON_PrintHeader() ◆ BlastPrintReference() void CBlastFormatUtil::BlastPrintReference ( bool html, size_t line_len, CNcbiOstream & out, blast::CReference::EPublication publication = blast::CReference::eGappedBlast, bool is_psiblast = false ) static ◆ BlastPrintVersionInfo() ◆ BlastXML2_FormatError() ◆ BlastXML2_FormatReport() [1/2] ◆ BlastXML2_FormatReport() [2/2] ◆ BlastXML2_PrintHeader() ◆ BlastXML_FormatReport()

Fills all fields in the XML BLAST output object.

Parameters: bxmlout XML BLAST output object [in] [out] data Data structure containing all information necessary to produce a BLAST XML report. out_stream for incremental output [out]

Referenced by CBlastFormat::x_PrintStructuredReport().

◆ CanGetTaxInfo() ◆ CBlastFormattingMatrix() CBlastFormattingMatrix::CBlastFormattingMatrix ( int ** data, unsigned int nrows, unsigned int ncols )

Constructor - allocates the matrix with appropriate size and populates with the values retrieved from a scoring matrix, passed in as a 2-dimensional integer array.

Definition at line 392 of file blastfmtutil.cpp.

References CSeqportUtil::Convert(), data, CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Ncbistdaa, CAliasBase< TPrim >::Get(), CSeq_data_Base::GetIupacaa(), int, max(), CNcbiMatrix< int >::Resize(), and row.

◆ CBlastHitMatrix()

Constructor.

Parameters: seqAligns input seqalign list height image height width image width format image type (png, bmp etc) font_path path to font files for rendering, the rendering library will look for the fonts in font_path + "/fonts"

Definition at line 87 of file blast_hitmatrix.cpp.

References format, ITERATE, CBlastHitMatrix::m_Aligns, CBlastHitMatrix::m_FileOut, CBlastHitMatrix::m_Format, CBlastHitMatrix::m_Height, CBlastHitMatrix::m_Renderer, CBlastHitMatrix::m_Thumbnail, CBlastHitMatrix::m_Width, and CBlastHitMatrix::x_InitGraphics().

◆ CreateSeqAnnotFromSeqAlignSet() ◆ Display() ◆ GetAlignment() virtual const objects::CSeq_align_set* IBlastXMLReportData::GetAlignment ( int query_index ) const pure virtual ◆ GetAlignmentSet() virtual CConstRef<objects::CSeq_align_set> IBlastXML2ReportData::GetAlignmentSet ( int num ) const pure virtual ◆ GetBl2seqMode() ◆ GetBlastProgramName() [1/2] virtual string IBlastXML2ReportData::GetBlastProgramName ( void ) const pure virtual ◆ GetBlastProgramName() [2/2] virtual string IBlastXMLReportData::GetBlastProgramName ( void ) const pure virtual ◆ GetBlastTask() [1/2] ◆ GetBlastTask() [2/2] ◆ GetCompositionBasedStats() ◆ GetDatabaseName() [1/2] virtual string IBlastXML2ReportData::GetDatabaseName ( void ) const pure virtual ◆ GetDatabaseName() [2/2] virtual string IBlastXMLReportData::GetDatabaseName ( void ) const pure virtual ◆ GetDbGeneticCode() virtual int IBlastXML2ReportData::GetDbGeneticCode ( void ) const pure virtual ◆ GetDbLength() [1/2] virtual Int8 IBlastXML2ReportData::GetDbLength ( void ) const pure virtual ◆ GetDbLength() [2/2] virtual Int8 IBlastXMLReportData::GetDbLength ( void ) const pure virtual ◆ GetDbNumSeqs() [1/2] virtual Int8 IBlastXML2ReportData::GetDbNumSeqs ( void ) const pure virtual ◆ GetDbNumSeqs() [2/2] virtual int IBlastXMLReportData::GetDbNumSeqs ( void ) const pure virtual ◆ GetEffectiveSearchSpace() [1/2] virtual Int8 IBlastXML2ReportData::GetEffectiveSearchSpace ( int num ) const pure virtual ◆ GetEffectiveSearchSpace() [2/2] virtual Int8 IBlastXMLReportData::GetEffectiveSearchSpace ( int query_index ) const pure virtual ◆ GetEntrezQuery() ◆ GetEntropy() [1/2] virtual double IBlastXML2ReportData::GetEntropy ( int num ) const pure virtual ◆ GetEntropy() [2/2] virtual double IBlastXMLReportData::GetEntropy ( int query_index ) const pure virtual ◆ GetErrorMessage() string CBlastHitMatrix::GetErrorMessage ( void ) inline ◆ GetEvalueThreshold() [1/2] virtual double IBlastXML2ReportData::GetEvalueThreshold ( void ) const pure virtual ◆ GetEvalueThreshold() [2/2] virtual double IBlastXMLReportData::GetEvalueThreshold ( void ) const pure virtual ◆ GetFilterString() [1/2] virtual string IBlastXML2ReportData::GetFilterString ( void ) const pure virtual ◆ GetFilterString() [2/2] virtual string IBlastXMLReportData::GetFilterString ( void ) const pure virtual ◆ GetGapExtensionCost() [1/2] virtual int IBlastXML2ReportData::GetGapExtensionCost ( void ) const pure virtual ◆ GetGapExtensionCost() [2/2] virtual int IBlastXMLReportData::GetGapExtensionCost ( void ) const pure virtual ◆ GetGapOpeningCost() [1/2] virtual int IBlastXML2ReportData::GetGapOpeningCost ( void ) const pure virtual ◆ GetGapOpeningCost() [2/2] virtual int IBlastXMLReportData::GetGapOpeningCost ( void ) const pure virtual ◆ GetGappedMode() virtual bool IBlastXMLReportData::GetGappedMode ( void ) const pure virtual ◆ GetKappa() [1/2] virtual double IBlastXML2ReportData::GetKappa ( int num ) const pure virtual ◆ GetKappa() [2/2] virtual double IBlastXMLReportData::GetKappa ( int query_index ) const pure virtual ◆ GetLambda() [1/2] virtual double IBlastXML2ReportData::GetLambda ( int num ) const pure virtual ◆ GetLambda() [2/2] virtual double IBlastXMLReportData::GetLambda ( int query_index ) const pure virtual ◆ GetLengthAdjustment() [1/2] virtual int IBlastXML2ReportData::GetLengthAdjustment ( int num ) const pure virtual ◆ GetLengthAdjustment() [2/2] virtual int IBlastXMLReportData::GetLengthAdjustment ( int query_index ) const pure virtual ◆ GetMaskLocations() [1/2] ◆ GetMaskLocations() [2/2] ◆ GetMasterGeneticCode() virtual int IBlastXMLReportData::GetMasterGeneticCode ( ) const pure virtual ◆ GetMatchReward() [1/2] virtual int IBlastXML2ReportData::GetMatchReward ( void ) const pure virtual ◆ GetMatchReward() [2/2] virtual int IBlastXMLReportData::GetMatchReward ( void ) const pure virtual ◆ GetMatrix() [1/2] ◆ GetMatrix() [2/2] ◆ GetMatrixName() [1/2] virtual string IBlastXML2ReportData::GetMatrixName ( void ) const pure virtual ◆ GetMatrixName() [2/2] virtual string IBlastXMLReportData::GetMatrixName ( void ) const pure virtual ◆ GetMessages() [1/2] virtual vector<string> IBlastXMLReportData::GetMessages ( ) const pure virtual ◆ GetMessages() [2/2] virtual string IBlastXML2ReportData::GetMessages ( int num ) const pure virtual ◆ GetMismatchPenalty() [1/2] virtual int IBlastXML2ReportData::GetMismatchPenalty ( void ) const pure virtual ◆ GetMismatchPenalty() [2/2] virtual int IBlastXMLReportData::GetMismatchPenalty ( void ) const pure virtual ◆ GetNetcacheID() string CBlastHitMatrix::GetNetcacheID ( void ) inline

Get netcache ID for the image stored in netcache.

Returns: : string netcache ID

Definition at line 122 of file blast_hitmatrix.hpp.

◆ GetNumOfSearchResults() ◆ GetNumQueries() virtual unsigned int IBlastXMLReportData::GetNumQueries ( void ) const pure virtual ◆ GetPHIPattern() [1/2] virtual string IBlastXML2ReportData::GetPHIPattern ( void ) const pure virtual ◆ GetPHIPattern() [2/2] virtual string IBlastXMLReportData::GetPHIPattern ( void ) const pure virtual ◆ GetQuery() virtual const objects::CSeq_loc* IBlastXMLReportData::GetQuery ( int query_index ) const pure virtual ◆ GetQueryGeneticCode() virtual int IBlastXML2ReportData::GetQueryGeneticCode ( void ) const pure virtual ◆ GetQuerySeqLoc() ◆ GetScope() [1/2] virtual objects::CScope* IBlastXMLReportData::GetScope ( int query_index ) const pure virtual ◆ GetScope() [2/2] virtual CRef<objects::CScope> IBlastXML2ReportData::GetScope ( void ) const pure virtual ◆ GetSlaveGeneticCode() virtual int IBlastXMLReportData::GetSlaveGeneticCode ( ) const pure virtual ◆ GetSubjectIds() ◆ GetWholeAlnSeqStrings() [1/2] void CBlastFormatUtil::GetWholeAlnSeqStrings ( string & query, string & masked_query, string & subject, const objects::CDense_seg & ds, objects::CScope & scope, int master_gen_code, int slave_gen_code, const ncbi::TMaskedQueryRegions & mask_info, align_format::CDisplaySeqalign::SeqLocCharOption mask_char, int query_frame ) static ◆ GetWholeAlnSeqStrings() [2/2] void CBlastFormatUtil::GetWholeAlnSeqStrings ( string & query, string & subject, const objects::CDense_seg & ds, objects::CScope & scope, int master_gen_code, int slave_gen_code ) static ◆ InsertSubjectScores()

Definition at line 572 of file blastfmtutil.cpp.

References _TRACE, CConstRef< C, Locker >::Empty(), CBlastFormatUtil::eNoQuerySubjCov, CBlastFormatUtil::eQueryCovPerSubj, CBlastFormatUtil::eQueryCovPerUniqSubj, CSeq_align_set_Base::Get(), CBioseq_Handle::GetCompleteBioseq(), CBioseq::GetLength(), COpenRange< Position >::GetLength(), CSeq_align_set_Base::IsSet(), CBioseq::IsSetLength(), COpenRange< Position >::NotEmpty(), and CSeq_align_set_Base::Set().

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastFormat::x_PrintTabularReport().

◆ IsBl2seq() ◆ IsFileOut() bool CBlastHitMatrix::IsFileOut ( void ) inline ◆ IsGappedSearch() ◆ IsIterativeSearch() ◆ PrintAsciiPssm() void CBlastFormatUtil::PrintAsciiPssm ( const objects::CPssmWithParameters & pssm, CConstRef< blast::CBlastAncillaryData > ancillary_data, CNcbiOstream & out ) static

Prints the PSSM in ASCII format (as in blastpgp's -Q option)

Parameters: pssm pssm to print [in] ancillary_data ancillary BLAST data to print [in] out output stream to write output to [in]

Definition at line 172 of file blastfmtutil.cpp.

References _ASSERT, AMINOACID_TO_NCBISTDAA, BLAST_SCORE_MIN, DIM, false, i, int, ITERATE, Blast_KarlinBlk::K, Blast_KarlinBlk::Lambda, NCBISTDAA_TO_AMINOACID, CConstRef< C, Locker >::NotEmpty(), out(), query, RESIDUE_ORDER, and rapidjson::value.

Referenced by CDeltaBlastApp::SavePssmToFile(), and CPsiBlastApp::SavePssmToFile().

◆ PrintDbInformation() ◆ SBlastXMLIncremental() SBlastXMLIncremental::SBlastXMLIncremental ( ) ◆ SetFileName() void CBlastHitMatrix::SetFileName ( string fileName ) inline ◆ SetThumbnail() void CBlastHitMatrix::SetThumbnail ( bool set ) inline ◆ WriteToFile() bool CBlastHitMatrix::WriteToFile ( void )

Outputs the image into the file (m_FileOut=true) or netcache.

Returns: : true if successful

Definition at line 211 of file blast_hitmatrix.cpp.

References CGlOsContext::GetBuffer(), CImage::GetData(), CBlastHitMatrix::IsFileOut(), CBlastHitMatrix::m_Context, CBlastHitMatrix::m_File, CBlastHitMatrix::m_Format, CBlastHitMatrix::m_Height, CBlastHitMatrix::m_ImageKey, CBlastHitMatrix::m_Width, CNetCacheAPI::PutData(), CImageIO::WriteImage(), and CBlastHitMatrix::x_RenderImage().

Referenced by CBlastHitMatrixCGIApplication::ProcessRequest().

◆ x_GetLabels() void CBlastHitMatrix::x_GetLabels ( void ) protected ◆ x_InitGraphics() void CBlastHitMatrix::x_InitGraphics ( const string & font_path = "" ) protected

Initialize rendering environment.

Definition at line 260 of file blast_hitmatrix.cpp.

References _TRACE, CFtglFontManager::Clear(), ERR_POST, Error(), eUnknown, CException::GetMsg(), CFtglFontManager::Instance(), CGlResMgr::Instance(), CRef< C, Locker >::IsNull(), CBlastHitMatrix::m_Context, CBlastHitMatrix::m_ErrorMessage, CBlastHitMatrix::m_Height, CBlastHitMatrix::m_Width, CGlOsContext::MakeCurrent(), NCBI_THROW, CRef< C, Locker >::Reset(), CFtglFontManager::SetDeviceResolution(), and CFtglFontManager::SetFontPath().

Referenced by CBlastHitMatrix::CBlastHitMatrix().

◆ x_InitObjectManager() void CBlastHitMatrix::x_InitObjectManager ( ) protected ◆ x_InitPort() void CBlastHitMatrix::x_InitPort ( ) protected

Initializes CGlPane.

Definition at line 62 of file blast_hitmatrix.cpp.

References CBioseq_Handle::GetBioseqLength(), CRange_Base::GetFrom(), COpenRange< Position >::GetToOpen(), CBlastHitMatrix::m_DataSource, CBlastHitMatrix::m_Height, CBlastHitMatrix::m_Port, CBlastHitMatrix::m_Width, CGlRect< T >::SetHorz(), CGlPane::SetModelLimitsRect(), CGlRect< T >::SetVert(), and CGlPane::SetViewport().

Referenced by CBlastHitMatrix::x_PreProcess().

◆ x_PreProcess() void CBlastHitMatrix::x_PreProcess ( void ) protected

Performs pre-processing for image rendering.

Definition at line 145 of file blast_hitmatrix.cpp.

References CHitMatrixDSBuilder::CreateDataSource(), CRef< C, Locker >::GetPointer(), CHitMatrixDSBuilder::Init(), CBlastHitMatrix::m_Aligns, CBlastHitMatrix::m_DataSource, CBlastHitMatrix::m_Port, CBlastHitMatrix::m_Renderer, CBlastHitMatrix::m_Scope, CBlastHitMatrix::m_Thumbnail, CBlastHitMatrix::x_GetLabels(), CBlastHitMatrix::x_InitObjectManager(), and CBlastHitMatrix::x_InitPort().

Referenced by CBlastHitMatrix::x_RenderImage().

◆ x_Render() void CBlastHitMatrix::x_Render ( void ) protected

Inits renderer display options and text labels.

Definition at line 170 of file blast_hitmatrix.cpp.

References CRuler::fHideLabels, CRuler::fShowTextLabel, CBlastHitMatrix::m_Aligns, CBlastHitMatrix::m_Height, CBlastHitMatrix::m_Port, CBlastHitMatrix::m_QueryID, CBlastHitMatrix::m_Renderer, CBlastHitMatrix::m_SubjectID, CBlastHitMatrix::m_Thumbnail, CBlastHitMatrix::m_Width, CGlPane::SetViewport(), and CGlPane::ZoomAll().

Referenced by CBlastHitMatrix::x_RenderImage().

◆ x_RenderImage() bool CBlastHitMatrix::x_RenderImage ( void ) protected

Renders a pairwise alignments between the first two Seq-id in the alignment.

Definition at line 228 of file blast_hitmatrix.cpp.

References IRender::Clear(), CImageUtil::FlipY(), GetGl(), CException::GetMsg(), CBlastHitMatrix::m_Context, CBlastHitMatrix::m_ErrorMessage, CBlastHitMatrix::m_Height, CBlastHitMatrix::m_Width, CGlOsContext::MakeCurrent(), CRef< C, Locker >::Reset(), CGlOsContext::SetBuffer(), CImage::SetDepth(), string, CException::what(), CBlastHitMatrix::x_PreProcess(), and CBlastHitMatrix::x_Render().

Referenced by CBlastHitMatrix::Display(), and CBlastHitMatrix::WriteToFile().

◆ ~CBlastHitMatrix() CBlastHitMatrix::~CBlastHitMatrix ( ) inline ◆ ~IBlastXML2ReportData() virtual IBlastXML2ReportData::~IBlastXML2ReportData ( ) inlinevirtual ◆ ~IBlastXMLReportData() virtual IBlastXMLReportData::~IBlastXMLReportData ( ) inlinevirtual ◆ m_Aligns ◆ m_Context ◆ m_DataSource ◆ m_ErrorMessage string CBlastHitMatrix::m_ErrorMessage private ◆ m_File string CBlastHitMatrix::m_File private ◆ m_FileOut bool CBlastHitMatrix::m_FileOut private ◆ m_Format ◆ m_Height int CBlastHitMatrix::m_Height private ◆ m_ImageKey string CBlastHitMatrix::m_ImageKey private ◆ m_IterationNum int SBlastXMLIncremental::m_IterationNum ◆ m_ObjMgr ◆ m_Port ◆ m_QueryID string CBlastHitMatrix::m_QueryID private ◆ m_Renderer ◆ m_Scope ◆ m_SerialXmlEnd string SBlastXMLIncremental::m_SerialXmlEnd ◆ m_SubjectID string CBlastHitMatrix::m_SubjectID private ◆ m_Thumbnail bool CBlastHitMatrix::m_Thumbnail private ◆ m_Width int CBlastHitMatrix::m_Width private

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