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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnmapprint_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/alnmgr/alnmapprint.cpp Source File

48

m_NumRows(aln_map.GetNumRows()),

68 m_Out

->setf(IOS_BASE::left, IOS_BASE::adjustfield);

78 m_Out

->setf(IOS_BASE::left, IOS_BASE::adjustfield);

87 m_Out

->setf(IOS_BASE::left, IOS_BASE::adjustfield);

123

m_Out

"\t"

<< seg <<

": "

;

169 for

(

int i

=0;

<chunk_vec->size();

++) {

172

m_Out

"[row"

row

"|"

"]"

;

173

m_Out

<< chunk->GetAlnRange().GetFrom() <<

"-" 174

<< chunk->GetAlnRange().GetTo() <<

" "

;

176 if

(!chunk->IsGap()) {

177

m_Out

<< chunk->GetRange().GetFrom() <<

"-" 178

<< chunk->GetRange().GetTo();

void PrintId(CAlnMap::TNumrow row) const

Field printers.

const CAlnMap::TNumrow m_NumRows

void Chunks(CAlnMap::TGetChunkFlags flags=CAlnMap::fAlnSegsOnly)

CAlnMapPrinter(const CAlnMap &aln_map, CNcbiOstream &out)

Constructor.

void CsvTable(char delim=',')

Printing methods.

const string & GetId(CAlnMap::TNumrow row) const

Fasta style Ids.

void PrintNumRow(CAlnMap::TNumrow row) const

void PrintSeqPos(TSeqPos pos) const

TSignedSeqPos GetStop(TNumrow row, TNumseg seg, int offset=0) const

TSegTypeFlags GetSegType(TNumrow row, TNumseg seg, int offset=0) const

TSignedSeqPos GetStart(TNumrow row, TNumseg seg, int offset=0) const

const CSeq_id & GetSeqId(TNumrow row) const

@ fUnalignedOnLeftOnAnchor

@ fUnalignedOnRightOnAnchor

@ fNotAlignedToSeqOnAnchor

TSeqPos GetAlnStop(TNumseg seg) const

CRef< CAlnChunkVec > GetAlnChunks(TNumrow row, const TSignedRange &range, TGetChunkFlags flags=fAlnSegsOnly) const

unsigned int TSegTypeFlags

TSeqPos GetLen(TNumseg seg, int offset=0) const

TSeqPos GetAlnStart(TNumseg seg) const

TNumseg GetNumSegs(void) const

static bool IsTypeInsert(TSegTypeFlags type)

std::ofstream out("events_result.xml")

main entry point for tests

unsigned int TSeqPos

Type for sequence locations and lengths.

const string AsFastaString(void) const

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

Magic spell ;-) needed for some weird compilers... very empiric.

#define row(bind, expected)

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