NCBI C++ ToolKit
Classes | Enumerations | Enumerator | Functions | Variables
BLAST Formatting
+ Collaboration diagram for BLAST Formatting:

Classes

class  CBlastFormatUtil
 setting up scope More...
 
class  CBlastFormattingMatrix
 256x256 matrix used for calculating positives etc. More...
 
struct  SBlastXMLIncremental
 Structure to hold data for incremental XML formatting. More...
 
class  IBlastXML2ReportData
 Interface for filling the top layer of the XML report. More...
 
class  IBlastXMLReportData
 Interface for filling the top layer of the XML report. More...
 
class  CBlastHitMatrix
 This class displays the image of the hitmatrix view for blast 2 seq results. More...
 

Enumerations

enum  CBlastFormatUtil::ESubjectScores { CBlastFormatUtil::eNoQuerySubjCov = 0 , CBlastFormatUtil::eQueryCovPerSubj = 0x01 , CBlastFormatUtil::eQueryCovPerUniqSubj = 0x02 , CBlastFormatUtil::eBothQuerySubjCov = eQueryCovPerSubj | eQueryCovPerUniqSubj }
 

Functions

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 CBlastFormattingMatrixIBlastXML2ReportData::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 TMaskedQueryRegionsIBlastXML2ReportData::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< stringIBlastXML2ReportData::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 CBlastFormattingMatrixIBlastXMLReportData::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 TMaskedQueryRegionsIBlastXMLReportData::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< stringIBlastXMLReportData::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...
 

Variables

int SBlastXMLIncremental::m_IterationNum
 ctor sets to true, set to false for first chunk. More...
 
string SBlastXMLIncremental::m_SerialXmlEnd
 tag to be printed at end. More...
 
CRef< CObjectManagerCBlastHitMatrix::m_ObjMgr
 Object manager. More...
 
CRef< CScopeCBlastHitMatrix::m_Scope
 Current scope. More...
 
vector< CConstRef< CSeq_align > > CBlastHitMatrix::m_Aligns
 Vector of seqaligns. More...
 
string CBlastHitMatrix::m_QueryID
 Query label id. More...
 
string CBlastHitMatrix::m_SubjectID
 Subject label id. More...
 
string CBlastHitMatrix::m_File
 File name. More...
 
bool CBlastHitMatrix::m_FileOut
 true if output to the file More...
 
bool CBlastHitMatrix::m_Thumbnail
 
int CBlastHitMatrix::m_Height
 Image height. More...
 
int CBlastHitMatrix::m_Width
 Image width. More...
 
CImageIO::EType CBlastHitMatrix::m_Format
 Image format (png,bmp etc) More...
 
string CBlastHitMatrix::m_ImageKey
 netcacheID More...
 
string CBlastHitMatrix::m_ErrorMessage
 Error message. More...
 
CIRef< IHitMatrixDataSourceCBlastHitMatrix::m_DataSource
 Renderer setup Parameter. More...
 
CGlPane CBlastHitMatrix::m_Port
 Renderer setup Parameter. More...
 
unique_ptr< CHitMatrixRendererCBlastHitMatrix::m_Renderer
 Renderer setup Parameter. More...
 
CRef< CGlOsContextCBlastHitMatrix::m_Context
 CGlOsContext context. More...
 

Detailed Description

Enumeration Type Documentation

◆ ESubjectScores

Enumerator
eNoQuerySubjCov 
eQueryCovPerSubj 
eQueryCovPerUniqSubj 
eBothQuerySubjCov 

Definition at line 180 of file blastfmtutil.hpp.

Function Documentation

◆ BlastGetVersion()

string CBlastFormatUtil::BlastGetVersion ( const string  program)
static

Returns the version and release date, e.g.

BLASTN 2.2.10 [Oct-19-2004]

Parameters
programType of BLAST program [in]

Definition at line 60 of file blastfmtutil.cpp.

References NStr::ToUpper().

Referenced by CBlastFormatUtil::BlastPrintVersionInfo(), BlastXML_FormatReport(), and s_FillBlastOutput().

◆ BlastJSON_FormatReport() [1/2]

void BlastJSON_FormatReport ( const IBlastXML2ReportData data,
CNcbiOstream out_stream 
)

◆ BlastJSON_FormatReport() [2/2]

void BlastJSON_FormatReport ( const IBlastXML2ReportData data,
string  file_name 
)

◆ BlastJSON_PrintHeader()

void BlastJSON_PrintHeader ( CNcbiOstream out_stream)

Definition at line 834 of file blastxml2_format.cpp.

Referenced by CBlastFormat::PrintProlog().

◆ BlastPrintReference()

void CBlastFormatUtil::BlastPrintReference ( bool  html,
size_t  line_len,
CNcbiOstream out,
blast::CReference::EPublication  publication = blast::CReference::eGappedBlast,
bool  is_psiblast = false 
)
static

Print out blast reference.

Parameters
htmlin html format or not
line_lenlength of each line desired
outstream to ouput
publicationWhich publication to show reference for? [in]
is_psiblastis this reference for psiblast? [in]

Definition at line 76 of file blastfmtutil.cpp.

References eDeltaBlast, IRegistry::Empty(), IRegistry::Get(), IRegistry::HasEntry(), out(), and str().

Referenced by CBlastFormat::PrintProlog().

◆ BlastPrintVersionInfo()

void CBlastFormatUtil::BlastPrintVersionInfo ( const string  program,
bool  html,
CNcbiOstream out 
)
static

Print out blast engine version.

Parameters
programname of blast program such as blastp, blastn
htmlin html format or not
outstream to ouput

Definition at line 66 of file blastfmtutil.cpp.

References CBlastFormatUtil::BlastGetVersion(), and out().

Referenced by CBlastFormat::PrintProlog().

◆ BlastXML2_FormatError()

void BlastXML2_FormatError ( int  exit_code,
string  err_msg,
CNcbiOstream out_stream 
)

Definition at line 805 of file blastxml2_format.cpp.

References kEmptyStr, and s_WriteXML2Object().

◆ BlastXML2_FormatReport() [1/2]

void BlastXML2_FormatReport ( const IBlastXML2ReportData data,
CNcbiOstream out_stream 
)

Fills all fields in the XML BLAST v2 output object.

Parameters
bxmloutXML BLAST v2 output object [in] [out]
dataData structure containing all information necessary to produce a BLAST XML report.[in]
out_streamoutput stream [out]

Fills all fields in the XML BLAST v2 output object.

Parameters
bxmloutBLAST XML report data structure to fill [in] [out]
dataData structure, from which all necessary information can be retrieved [in]
out_streamOutput stream for incremental output, ignore if NULL [out]

Definition at line 750 of file blastxml2_format.cpp.

References data, ERR_POST, Error(), CException::GetMsg(), s_FillBlastOutput(), s_WriteXML2ObjectNoHeader(), and CException::what().

Referenced by CBlastFormat::x_WriteXML2().

◆ BlastXML2_FormatReport() [2/2]

void BlastXML2_FormatReport ( const IBlastXML2ReportData data,
string  file_name 
)

◆ BlastXML2_PrintHeader()

void BlastXML2_PrintHeader ( CNcbiOstream out_stream)

Definition at line 781 of file blastxml2_format.cpp.

References eEncoding_Ascii, eNoOwnership, eSerialVerifyData_No, and string.

Referenced by CBlastFormat::PrintProlog().

◆ BlastXML_FormatReport()

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.

Parameters
bxmloutXML BLAST output object [in] [out]
dataData structure containing all information necessary to produce a BLAST XML report.
out_streamfor incremental output [out]

Referenced by CBlastFormat::x_PrintStructuredReport().

◆ CanGetTaxInfo()

virtual bool IBlastXML2ReportData::CanGetTaxInfo ( void  ) const
pure virtual

Implemented in CCmdLineBlastXML2ReportData.

◆ 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()

CBlastHitMatrix::CBlastHitMatrix ( const list< CRef< CSeq_align > > &  seqAligns,
int  height = 600,
int  width = 800,
CImageIO::EType  format = CImageIO::ePng,
const string font_path = "" 
)

Constructor.

Parameters
seqAlignsinput seqalign list
heightimage height
widthimage width
formatimage type (png, bmp etc)
font_pathpath 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()

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

◆ Display()

bool CBlastHitMatrix::Display ( CNcbiOstream out)

Outputs the image into CNcbiOstream.

Parameters
outstream to output
Returns
: true if successful

Definition at line 201 of file blast_hitmatrix.cpp.

References CGlOsContext::GetBuffer(), CBlastHitMatrix::m_Context, CBlastHitMatrix::m_Format, out(), CImageIO::WriteImage(), and CBlastHitMatrix::x_RenderImage().

Referenced by CBlastHitMatrixCGIApplication::ProcessRequest().

◆ GetAlignment()

virtual const objects::CSeq_align_set* IBlastXMLReportData::GetAlignment ( int  query_index) const
pure virtual

Returns set of alignments found for a given query.

Implemented in CCmdLineBlastXMLReportData.

◆ GetAlignmentSet()

virtual CConstRef<objects::CSeq_align_set> IBlastXML2ReportData::GetAlignmentSet ( int  num) const
pure virtual

Returns a vector continaing set of alignments found for a given query.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetBl2seqMode()

virtual string IBlastXML2ReportData::GetBl2seqMode ( void  ) const
pure virtual

Implemented in CCmdLineBlastXML2ReportData.

◆ GetBlastProgramName() [1/2]

virtual string IBlastXML2ReportData::GetBlastProgramName ( void  ) const
pure virtual

Returns BLAST program name as string.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetBlastProgramName() [2/2]

virtual string IBlastXMLReportData::GetBlastProgramName ( void  ) const
pure virtual

Returns BLAST program name as string.

Implemented in CCmdLineBlastXMLReportData.

◆ GetBlastTask() [1/2]

virtual blast::EProgram IBlastXML2ReportData::GetBlastTask ( void  ) const
pure virtual

Returns BLAST task as an enumerated value.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetBlastTask() [2/2]

virtual blast::EProgram IBlastXMLReportData::GetBlastTask ( void  ) const
pure virtual

Returns BLAST task as an enumerated value.

Implemented in CCmdLineBlastXMLReportData.

◆ GetCompositionBasedStats()

virtual int IBlastXML2ReportData::GetCompositionBasedStats ( void  ) const
pure virtual

Implemented in CCmdLineBlastXML2ReportData.

◆ GetDatabaseName() [1/2]

virtual string IBlastXML2ReportData::GetDatabaseName ( void  ) const
pure virtual

Returns database name.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetDatabaseName() [2/2]

virtual string IBlastXMLReportData::GetDatabaseName ( void  ) const
pure virtual

Returns database name.

Implemented in CCmdLineBlastXMLReportData.

◆ GetDbGeneticCode()

virtual int IBlastXML2ReportData::GetDbGeneticCode ( void  ) const
pure virtual

slave genetic code

Implemented in CCmdLineBlastXML2ReportData.

◆ GetDbLength() [1/2]

virtual Int8 IBlastXML2ReportData::GetDbLength ( void  ) const
pure virtual

Returns database length.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetDbLength() [2/2]

virtual Int8 IBlastXMLReportData::GetDbLength ( void  ) const
pure virtual

Returns database length.

Implemented in CCmdLineBlastXMLReportData.

◆ GetDbNumSeqs() [1/2]

virtual Int8 IBlastXML2ReportData::GetDbNumSeqs ( void  ) const
pure virtual

Returns number of database sequences.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetDbNumSeqs() [2/2]

virtual int IBlastXMLReportData::GetDbNumSeqs ( void  ) const
pure virtual

Returns number of database sequences.

Implemented in CCmdLineBlastXMLReportData.

◆ GetEffectiveSearchSpace() [1/2]

virtual Int8 IBlastXML2ReportData::GetEffectiveSearchSpace ( int  num) const
pure virtual

Returns effective search space for a given query.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetEffectiveSearchSpace() [2/2]

virtual Int8 IBlastXMLReportData::GetEffectiveSearchSpace ( int  query_index) const
pure virtual

Returns effective search space for a given query.

Implemented in CCmdLineBlastXMLReportData.

◆ GetEntrezQuery()

virtual string IBlastXML2ReportData::GetEntrezQuery ( void  ) const
pure virtual

Implemented in CCmdLineBlastXML2ReportData.

◆ GetEntropy() [1/2]

virtual double IBlastXML2ReportData::GetEntropy ( int  num) const
pure virtual

Returns Karlin-Altschul H parameter for a given query.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetEntropy() [2/2]

virtual double IBlastXMLReportData::GetEntropy ( int  query_index) const
pure virtual

Returns Karlin-Altschul H parameter for a given query.

Implemented in CCmdLineBlastXMLReportData.

◆ GetErrorMessage()

string CBlastHitMatrix::GetErrorMessage ( void  )
inline

Get error message.

Returns
: string error message

Definition at line 127 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrixCGIApplication::ProcessRequest().

◆ GetEvalueThreshold() [1/2]

virtual double IBlastXML2ReportData::GetEvalueThreshold ( void  ) const
pure virtual

Returns e-value theshold used in search.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetEvalueThreshold() [2/2]

virtual double IBlastXMLReportData::GetEvalueThreshold ( void  ) const
pure virtual

Returns e-value theshold used in search.

Implemented in CCmdLineBlastXMLReportData.

◆ GetFilterString() [1/2]

virtual string IBlastXML2ReportData::GetFilterString ( void  ) const
pure virtual

Returns filtering option string.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetFilterString() [2/2]

virtual string IBlastXMLReportData::GetFilterString ( void  ) const
pure virtual

Returns filtering option string.

Implemented in CCmdLineBlastXMLReportData.

◆ GetGapExtensionCost() [1/2]

virtual int IBlastXML2ReportData::GetGapExtensionCost ( void  ) const
pure virtual

Returns gap extension cost used in search.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetGapExtensionCost() [2/2]

virtual int IBlastXMLReportData::GetGapExtensionCost ( void  ) const
pure virtual

Returns gap extension cost used in search.

Implemented in CCmdLineBlastXMLReportData.

◆ GetGapOpeningCost() [1/2]

virtual int IBlastXML2ReportData::GetGapOpeningCost ( void  ) const
pure virtual

Returns gap opening cost used in search.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetGapOpeningCost() [2/2]

virtual int IBlastXMLReportData::GetGapOpeningCost ( void  ) const
pure virtual

Returns gap opening cost used in search.

Implemented in CCmdLineBlastXMLReportData.

◆ GetGappedMode()

virtual bool IBlastXMLReportData::GetGappedMode ( void  ) const
pure virtual

Returns true if search was gapped, false otherwise.

Implemented in CCmdLineBlastXMLReportData.

◆ GetKappa() [1/2]

virtual double IBlastXML2ReportData::GetKappa ( int  num) const
pure virtual

Returns Karlin-Altschul K parameter for a given query.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetKappa() [2/2]

virtual double IBlastXMLReportData::GetKappa ( int  query_index) const
pure virtual

Returns Karlin-Altschul K parameter for a given query.

Implemented in CCmdLineBlastXMLReportData.

◆ GetLambda() [1/2]

virtual double IBlastXML2ReportData::GetLambda ( int  num) const
pure virtual

Returns Karlin-Altschul Lambda parameter for a given query.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetLambda() [2/2]

virtual double IBlastXMLReportData::GetLambda ( int  query_index) const
pure virtual

Returns Karlin-Altschul Lambda parameter for a given query.

Implemented in CCmdLineBlastXMLReportData.

◆ GetLengthAdjustment() [1/2]

virtual int IBlastXML2ReportData::GetLengthAdjustment ( int  num) const
pure virtual

Returns length adjustment for a given query.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetLengthAdjustment() [2/2]

virtual int IBlastXMLReportData::GetLengthAdjustment ( int  query_index) const
pure virtual

Returns length adjustment for a given query.

Implemented in CCmdLineBlastXMLReportData.

◆ GetMaskLocations() [1/2]

virtual const TMaskedQueryRegions& IBlastXML2ReportData::GetMaskLocations ( ) const
pure virtual

Returns list of mask locations for a given query.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetMaskLocations() [2/2]

virtual const TMaskedQueryRegions* IBlastXMLReportData::GetMaskLocations ( int  query_index) const
pure virtual

Returns list of mask locations for a given query.

Implemented in CCmdLineBlastXMLReportData.

◆ GetMasterGeneticCode()

virtual int IBlastXMLReportData::GetMasterGeneticCode ( ) const
pure virtual

master genetic code

Implemented in CCmdLineBlastXMLReportData.

◆ GetMatchReward() [1/2]

virtual int IBlastXML2ReportData::GetMatchReward ( void  ) const
pure virtual

Returns match reward, for blastn search only.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetMatchReward() [2/2]

virtual int IBlastXMLReportData::GetMatchReward ( void  ) const
pure virtual

Returns match reward, for blastn search only.

Implemented in CCmdLineBlastXMLReportData.

◆ GetMatrix() [1/2]

virtual CBlastFormattingMatrix* IBlastXML2ReportData::GetMatrix ( void  ) const
pure virtual

Returns a 256x256 ASCII-alphabet matrix, needed for formatting.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetMatrix() [2/2]

virtual CBlastFormattingMatrix* IBlastXMLReportData::GetMatrix ( void  ) const
pure virtual

Returns a 256x256 ASCII-alphabet matrix, needed for formatting.

Implemented in CCmdLineBlastXMLReportData.

◆ GetMatrixName() [1/2]

virtual string IBlastXML2ReportData::GetMatrixName ( void  ) const
pure virtual

Returns matrix name.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetMatrixName() [2/2]

virtual string IBlastXMLReportData::GetMatrixName ( void  ) const
pure virtual

Returns matrix name.

Implemented in CCmdLineBlastXMLReportData.

◆ GetMessages() [1/2]

virtual vector<string> IBlastXMLReportData::GetMessages ( ) const
pure virtual

Get error messages, one element per query (e.g.

: size of return value == GetNumQueries());

Implemented in CCmdLineBlastXMLReportData.

◆ GetMessages() [2/2]

virtual string IBlastXML2ReportData::GetMessages ( int  num) const
pure virtual

Get error messages.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetMismatchPenalty() [1/2]

virtual int IBlastXML2ReportData::GetMismatchPenalty ( void  ) const
pure virtual

Returns mismatch penalty, for blastn search only.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetMismatchPenalty() [2/2]

virtual int IBlastXMLReportData::GetMismatchPenalty ( void  ) const
pure virtual

Returns mismatch penalty, for blastn search only.

Implemented in CCmdLineBlastXMLReportData.

◆ 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()

virtual int IBlastXML2ReportData::GetNumOfSearchResults ( void  ) const
pure virtual

Implemented in CCmdLineBlastXML2ReportData.

◆ GetNumQueries()

virtual unsigned int IBlastXMLReportData::GetNumQueries ( void  ) const
pure virtual

Returns number of query sequences.

Implemented in CCmdLineBlastXMLReportData.

◆ GetPHIPattern() [1/2]

virtual string IBlastXML2ReportData::GetPHIPattern ( void  ) const
pure virtual

Returns pattern string, for PHI BLAST search only.

Implemented in CCmdLineBlastXML2ReportData.

◆ GetPHIPattern() [2/2]

virtual string IBlastXMLReportData::GetPHIPattern ( void  ) const
pure virtual

Returns pattern string, for PHI BLAST search only.

Implemented in CCmdLineBlastXMLReportData.

◆ GetQuery()

virtual const objects::CSeq_loc* IBlastXMLReportData::GetQuery ( int  query_index) const
pure virtual

Returns a query Seq-loc for a given query index.

Implemented in CCmdLineBlastXMLReportData.

◆ GetQueryGeneticCode()

virtual int IBlastXML2ReportData::GetQueryGeneticCode ( void  ) const
pure virtual

master genetic code

Implemented in CCmdLineBlastXML2ReportData.

◆ GetQuerySeqLoc()

virtual CConstRef<objects::CSeq_loc> IBlastXML2ReportData::GetQuerySeqLoc ( void  ) const
pure virtual

Implemented in CCmdLineBlastXML2ReportData.

◆ GetScope() [1/2]

virtual objects::CScope* IBlastXMLReportData::GetScope ( int  query_index) const
pure virtual

Returns scope for a given query.

Implemented in CCmdLineBlastXMLReportData.

◆ GetScope() [2/2]

virtual CRef<objects::CScope> IBlastXML2ReportData::GetScope ( void  ) const
pure virtual

Returns scope .

Implemented in CCmdLineBlastXML2ReportData.

◆ GetSlaveGeneticCode()

virtual int IBlastXMLReportData::GetSlaveGeneticCode ( ) const
pure virtual

slave genetic code

Implemented in CCmdLineBlastXMLReportData.

◆ GetSubjectIds()

virtual list<string> IBlastXML2ReportData::GetSubjectIds ( void  ) const
pure virtual

Implemented in CCmdLineBlastXML2ReportData.

◆ 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()

void CBlastFormatUtil::InsertSubjectScores ( objects::CSeq_align_set &  org_align_set,
const objects::CBioseq_Handle &  query_handle,
TSeqRange  query_range = TSeqRange(),
ESubjectScores  score_type = eQueryCovPerSubj 
)
static

◆ IsBl2seq()

virtual bool IBlastXML2ReportData::IsBl2seq ( void  ) const
pure virtual

Implemented in CCmdLineBlastXML2ReportData.

◆ IsFileOut()

bool CBlastHitMatrix::IsFileOut ( void  )
inline

Checks if image is to be written to the file.

Returns
: true if image is to be written to the file

Definition at line 117 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrixCGIApplication::ProcessRequest(), and CBlastHitMatrix::WriteToFile().

◆ IsGappedSearch()

virtual bool IBlastXML2ReportData::IsGappedSearch ( void  ) const
pure virtual

Implemented in CCmdLineBlastXML2ReportData.

◆ IsIterativeSearch()

virtual bool IBlastXML2ReportData::IsIterativeSearch ( void  ) const
pure virtual

Implemented in CCmdLineBlastXML2ReportData.

◆ 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
pssmpssm to print [in]
ancillary_dataancillary BLAST data to print [in]
outoutput 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()

void CBlastFormatUtil::PrintDbInformation ( size_t  line_len,
string  definition_line,
int  nNumSeqs,
Uint8  nTotalLength,
bool  html,
bool  with_links,
CNcbiOstream out 
)
static

◆ SBlastXMLIncremental()

SBlastXMLIncremental::SBlastXMLIncremental ( )

Default ctor()

Definition at line 663 of file blastfmtutil.cpp.

References SBlastXMLIncremental::m_SerialXmlEnd.

◆ SetFileName()

void CBlastHitMatrix::SetFileName ( string  fileName)
inline

Inits file name if image is written to the file.

Parameters
fileNamefile name for image output

Definition at line 106 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrixCGIApplication::x_InitAppData().

◆ SetThumbnail()

void CBlastHitMatrix::SetThumbnail ( bool  set)
inline

Indicates that thumbmail should be shown.

Parameters
set

Definition at line 112 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrixCGIApplication::x_InitAppData().

◆ WriteToFile()

bool CBlastHitMatrix::WriteToFile ( void  )

◆ x_GetLabels()

void CBlastHitMatrix::x_GetLabels ( void  )
protected

◆ x_InitGraphics()

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

◆ x_InitObjectManager()

void CBlastHitMatrix::x_InitObjectManager ( )
protected

◆ x_InitPort()

void CBlastHitMatrix::x_InitPort ( )
protected

◆ x_PreProcess()

void CBlastHitMatrix::x_PreProcess ( void  )
protected

◆ x_Render()

void CBlastHitMatrix::x_Render ( void  )
protected

◆ x_RenderImage()

bool CBlastHitMatrix::x_RenderImage ( void  )
protected

◆ ~CBlastHitMatrix()

CBlastHitMatrix::~CBlastHitMatrix ( )
inline

Destructor.

Definition at line 101 of file blast_hitmatrix.hpp.

◆ ~IBlastXML2ReportData()

virtual IBlastXML2ReportData::~IBlastXML2ReportData ( )
inlinevirtual

Our virtual destructor.

Definition at line 58 of file blastxml2_format.hpp.

◆ ~IBlastXMLReportData()

virtual IBlastXMLReportData::~IBlastXMLReportData ( )
inlinevirtual

Our virtual destructor.

Definition at line 59 of file blastxml_format.hpp.

Variable Documentation

◆ m_Aligns

vector< CConstRef<CSeq_align> > CBlastHitMatrix::m_Aligns
private

◆ m_Context

CRef<CGlOsContext> CBlastHitMatrix::m_Context
private

◆ m_DataSource

CIRef<IHitMatrixDataSource> CBlastHitMatrix::m_DataSource
private

Renderer setup Parameter.

Definition at line 203 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrix::x_InitPort(), and CBlastHitMatrix::x_PreProcess().

◆ m_ErrorMessage

string CBlastHitMatrix::m_ErrorMessage
private

Error message.

Definition at line 200 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrix::x_InitGraphics(), and CBlastHitMatrix::x_RenderImage().

◆ m_File

string CBlastHitMatrix::m_File
private

File name.

Definition at line 180 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrix::WriteToFile().

◆ m_FileOut

bool CBlastHitMatrix::m_FileOut
private

true if output to the file

Definition at line 183 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrix::CBlastHitMatrix().

◆ m_Format

CImageIO::EType CBlastHitMatrix::m_Format
private

◆ m_Height

int CBlastHitMatrix::m_Height
private

◆ m_ImageKey

string CBlastHitMatrix::m_ImageKey
private

netcacheID

Definition at line 197 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrix::WriteToFile().

◆ m_IterationNum

int SBlastXMLIncremental::m_IterationNum

ctor sets to true, set to false for first chunk.

Definition at line 212 of file blastfmtutil.hpp.

Referenced by BlastXML_FormatReport().

◆ m_ObjMgr

CRef<CObjectManager> CBlastHitMatrix::m_ObjMgr
private

Object manager.

Definition at line 165 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrix::x_InitObjectManager().

◆ m_Port

CGlPane CBlastHitMatrix::m_Port
private

Renderer setup Parameter.

Definition at line 206 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrix::x_InitPort(), CBlastHitMatrix::x_PreProcess(), and CBlastHitMatrix::x_Render().

◆ m_QueryID

string CBlastHitMatrix::m_QueryID
private

Query label id.

Definition at line 174 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrix::x_GetLabels(), and CBlastHitMatrix::x_Render().

◆ m_Renderer

unique_ptr<CHitMatrixRenderer> CBlastHitMatrix::m_Renderer
private

Renderer setup Parameter.

Definition at line 209 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrix::CBlastHitMatrix(), CBlastHitMatrix::x_PreProcess(), and CBlastHitMatrix::x_Render().

◆ m_Scope

CRef<CScope> CBlastHitMatrix::m_Scope
private

◆ m_SerialXmlEnd

string SBlastXMLIncremental::m_SerialXmlEnd

tag to be printed at end.

Definition at line 215 of file blastfmtutil.hpp.

Referenced by BlastXML_FormatReport(), CBlastFormat::PrintEpilog(), and SBlastXMLIncremental::SBlastXMLIncremental().

◆ m_SubjectID

string CBlastHitMatrix::m_SubjectID
private

Subject label id.

Definition at line 177 of file blast_hitmatrix.hpp.

Referenced by CBlastHitMatrix::x_GetLabels(), and CBlastHitMatrix::x_Render().

◆ m_Thumbnail

bool CBlastHitMatrix::m_Thumbnail
private

◆ m_Width

int CBlastHitMatrix::m_Width
private
Modified on Fri Jun 14 16:49:03 2024 by modify_doxy.py rev. 669887