src/objtools/align_format/showdefline.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbiexpt.hpp>
#include <corelib/ncbiutil.hpp>
#include <corelib/ncbistre.hpp>
#include <corelib/ncbireg.hpp>
#include <serial/objostrasnb.hpp>
#include <serial/objistrasnb.hpp>
#include <connect/ncbi_conn_stream.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Dbtag.hpp>
#include <serial/iterator.hpp>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
#include <serial/serial.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/seqalign/Std_seg.hpp>
#include <objects/seqalign/Dense_diag.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/blastdb/Blast_def_line.hpp>
#include <objects/blastdb/Blast_def_line_set.hpp>
#include <objects/blastdb/defline_extra.hpp>
#include <objtools/align_format/showdefline.hpp>
#include <stdio.h>
#include <html/htmlhelper.hpp>

Include dependency graph for showdefline.cpp:

Go to the source code of this file.

Functions
	USING_SCOPE (objects)
	USING_SCOPE (sequence)
static string	s_GetIdUrl (const CBioseq::TId &ids, int gi, string &user_url, bool is_db_na, string &db_name, bool open_new_window, string &rid, int query_number, int taxid, int linkout, int cur_align)
	Return url for seqid.
static void	s_DisplayDescrColumnHeader (CNcbiOstream &out, int currDisplaySort, string query_buf, int columnDisplSort, int columnHspSort, string columnText, int max_data_len, bool html)
Variables
static char const	rcsid [] = "$Id: showdefline.cpp 175746 2009-11-10 15:00:18Z madden $"
static string	kOneSpaceMargin = " "
static string	kTwoSpaceMargin = " "
static const string	kHeader = "Sequences producing significant alignments:"
static const string	kScore = "Score"
static const string	kE = "E"
static const string	kBits
static const string	kEvalue = "E value"
static const string	kValue = "Value"
static const string	kN = "N"
static const string	kRepeatHeader = "Sequences used in model and found again:"
static const string	kNewSeqHeader
static const string	kMaxScore = "Max score"
static const string	kTotalScore = "Total score"
static const string	kTotal = "Total"
static const string	kIdentity = "Max ident"
static const string	kPercent = "Percent"
static const string	kHighest = "Highest"
static const string	kQuery = "Query"
static const string	kCoverage = "Query coverage"
static const string	kEllipsis = "..."
static const string	kPsiblastNewSeqGif
static const string	kPsiblastNewSeqBackgroundGif
static const string	kPsiblastCheckedBackgroundGif
static const string	kPsiblastCheckedGif
static const string	kPsiblastEvalueLink = "<a name = Evalue></a>"
static const string	kPsiblastCheckboxChecked
static const string	kPsiblastCheckbox

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Function Documentation

static void s_DisplayDescrColumnHeader (  CNcbiOstream &  out, int  currDisplaySort, string  query_buf, int  columnDisplSort, int  columnHspSort, string  columnText, int  max_data_len, bool  html )  [static]

Definition at line 883 of file showdefline.cpp. References CAlignFormatUtil::AddSpace(). Referenced by CShowBlastDefline::x_DisplayDeflineTable().

static string s_GetIdUrl (  const CBioseq::TId &  ids, int  gi, string &  user_url, bool  is_db_na, string &  db_name, bool  open_new_window, string &  rid, int  query_number, int  taxid, int  linkout, int  cur_align )  [static]

Return url for seqid. Parameters: ids,:  input seqid list gi,:  gi to use user_url,:  use this user specified url if it's non-empty is_db_na,:  is the database nucleotide or not db_name,:  name of the database open_new_window,:  click the url to open a new window? rid,:  RID query_number,:  the query number cur_align,:  index of the current alignment Definition at line 145 of file showdefline.cpp. References CAlignFormatUtil::BuildSRAUrl(), eHitInMapviewer, FindBestChoice(), NcbiEmptyString, and CSeq_id::WorstRank().

USING_SCOPE (  sequence   )

USING_SCOPE (  objects   )

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Variable Documentation

const string kBits [static]

Initial value: (getenv("CTOOLKIT_COMPATIBLE") ? "(bits)" : "(Bits)") Definition at line 93 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), and CShowBlastDefline::x_InitDefline().

const string kCoverage = "Query coverage" [static]

Definition at line 108 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDeflineTable(), and CShowBlastDefline::x_InitDeflineTable().

const string kE = "E" [static]

Definition at line 92 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline().

const string kEllipsis = "..." [static]

Definition at line 109 of file showdefline.cpp. Referenced by RemovePeriodFromEnd(), and CShowBlastDefline::x_DisplayDefline().

const string kEvalue = "E value" [static]

Definition at line 95 of file showdefline.cpp. Referenced by BOOST_AUTO_TEST_CASE(), LinkHspTestFixture::testUnevenGapLinkHsps(), and CShowBlastDefline::x_DisplayDeflineTable().

const string kHeader = "Sequences producing significant alignments:" [static]

Definition at line 90 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), and CShowBlastDefline::x_DisplayDeflineTable().

const string kHighest = "Highest" [static]

Definition at line 106 of file showdefline.cpp.

const string kIdentity = "Max ident" [static]

Definition at line 104 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDeflineTable(), and CShowBlastDefline::x_InitDeflineTable().

const string kMaxScore = "Max score" [static]

Definition at line 101 of file showdefline.cpp. Referenced by BOOST_AUTO_TEST_CASE(), CQualityScoringMethod::GetColorForScore(), CShowBlastDefline::x_DisplayDeflineTable(), and CShowBlastDefline::x_InitDeflineTable().

const string kN = "N" [static]

Definition at line 97 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), and CShowBlastDefline::x_DisplayDeflineTable().

const string kNewSeqHeader [static]

Initial value: "Sequences not found previously or not pr\ eviously below threshold:" Definition at line 99 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline().

string kOneSpaceMargin = " " [static]

Definition at line 86 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), and CShowBlastDefline::x_DisplayDeflineTable().

const string kPercent = "Percent" [static]

Definition at line 105 of file showdefline.cpp.

const string kPsiblastCheckbox [static]

Initial value: "<INPUT TYPE=\"checkbox\" NAME=\"ch\ ecked_GI\" VALUE=\"%d\"> " Definition at line 130 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), and CShowBlastDefline::x_DisplayDeflineTable().

const string kPsiblastCheckboxChecked [static]

Initial value: "<INPUT TYPE=\"checkbox\" NAME\ =\"checked_GI\" VALUE=\"%d\" CHECKED> <INPUT TYPE=\"hidden\" NAME =\"good_G\ I\" VALUE = \"%d\">" Definition at line 126 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), and CShowBlastDefline::x_DisplayDeflineTable().

const string kPsiblastCheckedBackgroundGif [static]

Initial value: "<IMG SRC=\"images\ /bg.gif\" WIDTH=15 HEIGHT=15 ALT=\" \">" Definition at line 118 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), and CShowBlastDefline::x_DisplayDeflineTable().

const string kPsiblastCheckedGif [static]

Initial value: "<IMG SRC=\"images/checked.g\ if\" WIDTH=15 HEIGHT=15 ALT=\"Checked mark\">" Definition at line 121 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), and CShowBlastDefline::x_DisplayDeflineTable().

const string kPsiblastEvalueLink = "<a name = Evalue></a>" [static]

Definition at line 124 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), and CShowBlastDefline::x_DisplayDeflineTable().

const string kPsiblastNewSeqBackgroundGif [static]

Initial value: "<IMG SRC=\"images/\ bg.gif\" WIDTH=30 HEIGHT=15 ALT=\" \">" Definition at line 115 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), and CShowBlastDefline::x_DisplayDeflineTable().

const string kPsiblastNewSeqGif [static]

Initial value: "<IMG SRC=\"images/new.gif\" \ WIDTH=30 HEIGHT=15 ALT=\"New sequence mark\">" Definition at line 112 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), and CShowBlastDefline::x_DisplayDeflineTable().

const string kQuery = "Query" [static]

Definition at line 107 of file showdefline.cpp. Referenced by BOOST_AUTO_TEST_CASE(), CPssmInputFlankingGaps::CPssmInputFlankingGaps(), CPssmInputTestData::SetupDuplicateHit(), CPssmInputTestData::SetupHenikoffsPositionBasedSequenceWeights(), CPssmInputTestData::SetupMsaHasUnalignedRegion(), CPsiBlastInputClustalW::x_ExtractQueryFromMsa(), and CDisplaySeqalign::x_FillSeqid().

const string kRepeatHeader = "Sequences used in model and found again:" [static]

Definition at line 98 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline().

const string kScore = "Score" [static]

Definition at line 91 of file showdefline.cpp. Referenced by BOOST_AUTO_TEST_CASE(), checkReevaluateResultsGapped(), checkReevaluateResultsUngappedNucl(), checkReevaluateResultsUngappedTransl(), s_BuildScoreList(), and CShowBlastDefline::x_DisplayDefline().

const string kTotal = "Total" [static]

Definition at line 103 of file showdefline.cpp. Referenced by BOOST_AUTO_TEST_CASE(), and CShowBlastDefline::x_InitDeflineTable().

const string kTotalScore = "Total score" [static]

Definition at line 102 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDeflineTable().

string kTwoSpaceMargin = " " [static]

Definition at line 87 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline().

const string kValue = "Value" [static]

Definition at line 96 of file showdefline.cpp. Referenced by CShowBlastDefline::x_DisplayDefline(), CShowBlastDefline::x_InitDefline(), and CShowBlastDefline::x_InitDeflineTable().

char const rcsid[] = "$Id: showdefline.cpp 175746 2009-11-10 15:00:18Z madden $" [static]

Definition at line 34 of file showdefline.cpp.

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