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/** \file
\brief The TUReadSeq class
*/
#include "TUReadSeq.h"
TUReadSeq::TUReadSeq ( wxString _filename )
{
error = 0 ;
filename = _filename ;
getFormat () ;
getSequenceNames() ;
getSequences () ;
if ( seqs.GetCount() == 0 ) error = 1 ;
}
void TUReadSeq::getFormat ()
{
if ( error != 0 ) return ;
format = seqFileFormat ( filename.mb_str() , &skiplines , &error ) ;
if ( format < kMinFormat || format > kMaxFormat ) error = 1 ;
}
int TUReadSeq::getSequenceNames ()
{
if ( error != 0 ) return 0 ;
char *seqlist; /* list of sequence names, newline separated, 0 terminated */
seqlist = listSeqs( filename.mb_str(), skiplines, format, &numseqs, &error);
wxString s ( seqlist , *wxConvCurrent ) ;
free( seqlist);
explode ( _T("\n") , s , seq_names ) ;
return seq_names.GetCount() ;
}
void TUReadSeq::getSequences ()
{
if ( error != 0 ) return ;
short seqIndex ;
seqs.Clear () ;
for ( seqIndex = 1 ; error == 0 && seqIndex <= seq_names.GetCount() ; seqIndex++ )
{
long seqlen; /* length of seq */
char seqid[256]; /* sequence name */
char *seq; /* sequence, 0 terminated, free when done */
seqid[0] = 0 ;
seq = readSeq( seqIndex, filename.mb_str(), skiplines, format,
&seqlen, &numseqs, &error, seqid);
for ( char *c = seq ; *c ; c++ )
{
if ( *c >= 'a' && *c <= 'z' ) *c = *c - 'a' + 'A' ;
}
seq_names[seqIndex-1] = wxString ( seqid , *wxConvCurrent ) ;
seqs.Add ( wxString ( seq , *wxConvCurrent) ) ;
free(seq);
}
}
int TUReadSeq::getSeqType ( wxString t )
{
short i = getseqtype ( t.mb_str() , t.length() ) ;
if ( i == kAmino ) return TYPE_AMINO_ACIDS ;
return TYPE_VECTOR ;
}
void TUReadSeq::convert ( TGenBank &gb )
{
wxString s ;
for ( int a = 0 ; a < seqs.GetCount() ; a++ )
{
s += _T("LOCUS ") + seq_names[a] + _T("\n") ;
s += _T("TITLE ") + seq_names[a] + _T("\n") ;
s += _T("ORIGIN\n") ;
s += _T(" ") + seqs[a] + _T("\n") ;
s += _T("//\n") ;
}
gb.paste ( s ) ;
}
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