NCBI C++ ToolKit
Functions | Variables
blast_format.cpp File Reference
#include <ncbi_pch.hpp>
#include <algo/blast/format/blast_format.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/create_defline.hpp>
#include <algo/blast/core/blast_stat.h>
#include <corelib/ncbiutil.hpp>
#include <algo/blast/api/sseqloc.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/format/blastxml_format.hpp>
#include <algo/blast/format/data4xmlformat.hpp>
#include <algo/blast/format/blastxml2_format.hpp>
#include <algo/blast/format/data4xml2format.hpp>
#include <algo/blast/format/build_archive.hpp>
#include <misc/jsonwrapp/jsonwrapp.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <serial/objostrxml.hpp>
#include <corelib/ncbistre.hpp>
+ Include dependency graph for blast_format.cpp:

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Functions

 USING_SCOPE (blast)
 
 USING_SCOPE (objects)
 
 USING_SCOPE (align_format)
 
 USING_SCOPE (sequence)
 
static bool s_HasLocalIDs (CConstRef< CBlastQueryVector > queries)
 Auxialiary function to determine if there are local IDs in the identifiers of the query sequences. More...
 
bool s_IsGlobalSeqAlign (CConstRef< objects::CSeq_align_set > seqalign_set)
 
int s_SetFlags (string &program, blast::CFormattingArgs::EOutputFormat format_type, bool html, bool showgi, bool isbl2seq, bool disableKAStats)
 
static void s_SetCloneInfo (const CIgBlastTabularInfo &tabinfo, const CBioseq_Handle &handle, CBlastFormat::SClone &clone_info)
 
static string s_GetMolType (const CBioseq_Handle &bioseqHandle)
 
static string s_GetBaseName (const string &baseFile, bool isXML, bool withPath)
 
bool s_SetCompBasedStats (EProgram program)
 

Variables

 USING_NCBI_SCOPE
 
static const string kHTML_Prefix
 
static const string kHTML_Suffix
 

Function Documentation

◆ s_GetBaseName()

static string s_GetBaseName ( const string baseFile,
bool  isXML,
bool  withPath 
)
static

◆ s_GetMolType()

static string s_GetMolType ( const CBioseq_Handle bioseqHandle)
static

◆ s_HasLocalIDs()

static bool s_HasLocalIDs ( CConstRef< CBlastQueryVector queries)
static

Auxialiary function to determine if there are local IDs in the identifiers of the query sequences.

Parameters
queriesquery sequence(s) [in]

Definition at line 475 of file blast_format.cpp.

References IsLocalId(), and ITERATE.

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

◆ s_IsGlobalSeqAlign()

bool s_IsGlobalSeqAlign ( CConstRef< objects::CSeq_align_set >  seqalign_set)

Definition at line 549 of file blast_format.cpp.

References CSeq_align_Base::eType_global.

Referenced by CBlastFormat::PrintOneResultSet().

◆ s_SetCloneInfo()

static void s_SetCloneInfo ( const CIgBlastTabularInfo tabinfo,
const CBioseq_Handle handle,
CBlastFormat::SClone clone_info 
)
static

◆ s_SetCompBasedStats()

bool s_SetCompBasedStats ( EProgram  program)

◆ s_SetFlags()

int s_SetFlags ( string program,
blast::CFormattingArgs::EOutputFormat  format_type,
bool  html,
bool  showgi,
bool  isbl2seq,
bool  disableKAStats 
)

◆ USING_SCOPE() [1/4]

USING_SCOPE ( align_format  )

◆ USING_SCOPE() [2/4]

USING_SCOPE ( blast  )

◆ USING_SCOPE() [3/4]

USING_SCOPE ( objects  )

◆ USING_SCOPE() [4/4]

USING_SCOPE ( sequence  )

Variable Documentation

◆ kHTML_Prefix

const string kHTML_Prefix
static
Initial value:
=
"<HTML>\n"
"<HEAD><TITLE>BLAST Search Results</TITLE></HEAD>\n"
"<BODY BGCOLOR=\"#FFFFFF\" LINK=\"#0000FF\" VLINK=\"#660099\" ALINK=\"#660099\">\n"
"<PRE>\n"

Definition at line 326 of file blast_format.cpp.

Referenced by CBlastFormat::PrintProlog().

◆ kHTML_Suffix

const string kHTML_Suffix
static
Initial value:
=
"</PRE>\n"
"</BODY>\n"
"</HTML>"

Definition at line 332 of file blast_format.cpp.

Referenced by CBlastFormat::PrintEpilog().

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 60 of file blast_format.cpp.

Modified on Wed Jun 19 17:02:27 2024 by modify_doxy.py rev. 669887