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NCBI C++ ToolKit: AlignmentDisplay Class Reference

Search Toolkit Book for AlignmentDisplay

#include <objtools/cddalignview/cav_alndisplay.hpp>

AlignmentDisplay (const SequenceSet *sequenceSet, const AlignmentSet *alignmentSet) ~AlignmentDisplay () unsigned int GetWidth (void) const unsigned int GetNRows (void) const char GetCharAt (int alnLoc, int row) const int GetFirstAlignedLoc (void) const int GetLastAlignedLoc (void) const const string GetColumnColor (int alnLoc, double conservationThreshhold) const int DumpText (CNcbiOstream &os, unsigned int options, int firstCol, int lastCol, int nColumns, double conservationThreshhold=2.0, const char *titleHTML=NULL, int nFeatures=0, const AlignmentFeature *alnFeatures=NULL) const int DumpCondensed (CNcbiOstream &os, unsigned int options, int firstCol, int lastCol, int nColumns, double conservationThreshhold=2.0, const char *titleHTML=NULL, int nFeatures=0, const AlignmentFeature *alnFeatures=NULL) const int DumpFASTA (int firstCol, int lastCol, int nColumns, bool doLowercase, CNcbiOstream &outStream) const int Status (void) const

Definition at line 92 of file cav_alndisplay.hpp.

◆ IndexAlnLocToSeqLocRows ◆ TextRows ◆ AlignmentDisplay()

Definition at line 90 of file cav_alndisplay.cpp.

References a, AlignmentSet::alignments, CAV_SUCCESS, ERR_POST_X, Error(), firstAlnLoc, GetCharAt(), GetNRows(), GetWidth(), i, indexAlnLocToSeqLocRows, Info(), InsertGaps(), int, IsAligned(), l(), lastAlnLoc, SequenceSet::master, Sequence::sequenceString, SplitUnaligned(), Squeeze(), status, StrToLower(), textRows, tolower(), and toupper().

◆ ~AlignmentDisplay() AlignmentDisplay::~AlignmentDisplay ( ) ◆ DumpCondensed()

Definition at line 490 of file cav_alndisplay.cpp.

References bgColor, blockBGColors, CAV_ANNOT_BOTTOM, CAV_ERROR_BAD_PARAMS, CAV_HTML, CAV_HTML_HEADER, CAV_NO_PARAG_COLOR, ERR_POST_X, Error(), GetCharAt(), GetColumnColor(), GetNRows(), GetWidth(), i, indexAlnLocToSeqLocRows, Info(), int, IsAligned(), IsGap(), AlignmentFeature::locations, log10(), n, nBlockColors, row, ShortAndEscapedString(), ncbi::grid::netcache::search::fields::size, string, t, and textRows.

◆ DumpFASTA() ◆ DumpText() ◆ GetCharAt() char AlignmentDisplay::GetCharAt ( int alnLoc, int row ) const

Definition at line 391 of file cav_alndisplay.cpp.

References ERR_POST_X, Error(), GetNRows(), GetWidth(), row, and textRows.

Referenced by AlignmentDisplay(), DumpCondensed(), ShiftUnalignedLeft(), SplitUnaligned(), Squeeze(), and VerifyAlignmentData().

◆ GetColumnColor() const string AlignmentDisplay::GetColumnColor ( int alnLoc, double conservationThreshhold ) const ◆ GetFirstAlignedLoc() int AlignmentDisplay::GetFirstAlignedLoc ( void ) const inline ◆ GetLastAlignedLoc() int AlignmentDisplay::GetLastAlignedLoc ( void ) const inline ◆ GetNRows() unsigned int AlignmentDisplay::GetNRows ( void ) const inline ◆ GetWidth() unsigned int AlignmentDisplay::GetWidth ( void ) const inline ◆ InsertGaps() void AlignmentDisplay::InsertGaps ( int nGaps, int beforePos ) private ◆ ShiftUnalignedLeft() void AlignmentDisplay::ShiftUnalignedLeft ( void ) private ◆ SplitUnaligned() void AlignmentDisplay::SplitUnaligned ( void ) private ◆ Squeeze() void AlignmentDisplay::Squeeze ( void ) private ◆ Status() int AlignmentDisplay::Status ( void ) const inline ◆ firstAlnLoc int AlignmentDisplay::firstAlnLoc private ◆ indexAlnLocToSeqLocRows ◆ lastAlnLoc int AlignmentDisplay::lastAlnLoc private ◆ SHOW_IDENTITY const double AlignmentDisplay::SHOW_IDENTITY = 100000.0 static ◆ status int AlignmentDisplay::status private ◆ textRows

The documentation for this class was generated from the following files:

include/objtools/cddalignview/cav_alndisplay.hpp
src/objtools/cddalignview/cav_alndisplay.cpp

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