/*!
Returns a list with the names of all properties for this class.
If \a super is TRUE, inherited properties are included.
\sa property()
*/
QStrList QMetaObject::propertyNames( bool super ) const
{
QStrList l( FALSE );
if ( superclass && super ) {
QStrList sl = superclass->propertyNames( super );
for ( QStrListIterator slit( sl ); slit.current(); ++slit )
l.append( slit.current() );
}
for( int i = 0; i < d->numPropData; ++i ) {
if ( d->propData[i].isValid() )
l.append( d->propData[i].name() );
}
return l;
}
/*!\internal
*/
QStrList QMetaObject::enumeratorNames( bool super ) const
{
QStrList l( FALSE );
if ( superclass && super ) {
QStrList sl = superclass->enumeratorNames( super );
for ( QStrListIterator slit( sl ); slit.current(); ++slit )
l.append( slit.current() );
}
for( int i = 0; i < d->numEnumData; ++i ) {
if ( d->enumData[i].items )
l.append( d->enumData[i].name );
}
return l;
}
//trims exons around internal alignment gaps to complete codons
//if CDS can be retrieved from bioseq
void CSplignTrim::TrimHolesToCodons(TSegs& segments, CBioseq_Handle& mrna_bio_handle, bool mrna_strand, size_t mrna_len)
{
if( mrna_bio_handle ) {
//collect CDS intervals (could be more than one in a case of ribosomal slippage)
vector<TSeqRange> tr;
for(CFeat_CI ci(mrna_bio_handle, SAnnotSelector(CSeqFeatData::e_Cdregion)); ci; ++ci) {
for(CSeq_loc_CI slit(ci->GetLocation()); slit; ++slit) {
TSeqRange r, ori;
ori = slit.GetRange();
if( mrna_strand ) {
r = ori;
} else {//reverse
r.SetFrom(mrna_len - ori.GetTo() - 1);
r.SetTo(mrna_len - ori.GetFrom() - 1);
}
tr.push_back(r);
}
}
if(tr.empty()) return;// CDS not found
//trim
AdjustGaps(segments);//make sure there is no adjacent gaps
size_t pos1 = 0, pos2 = 2;
for(; pos2 < segments.size(); ++pos1, ++pos2) {
if( segments[pos1].m_exon && !segments[pos1+1].m_exon && segments[pos2].m_exon ) {//candidate for trimming
//trim left exon
TSeqPos p1 = segments[pos1].m_box[1];
ITERATE(vector<TSeqRange>, it, tr) {
if( p1 >= it->GetFrom() && p1 <= it->GetTo() ) {
TSeqPos cut_mrna_len = (p1 + 1 - it->GetFrom()) % 3, cnt = 0;
string transcript = segments[pos1].m_details;
int i = (int)transcript.size() - 1;
for(; i>=0; --i) {
if( cnt%3 == cut_mrna_len && transcript[i] == 'M' ) { //cut point
CutFromRight(transcript.size() - i - 1, segments[pos1]);
break;
}
if( transcript[i] != 'I' ) ++cnt;
}
if( i < 0 ) {// exon should not be so bad
NCBI_THROW(CAlgoAlignException, eInternal, g_msg_InvalidRange);
}
break;
}
}
//trim right exon
TSeqPos p2 = segments[pos2].m_box[0];
ITERATE(vector<TSeqRange>, it, tr) {
if( p2 >= it->GetFrom() && p2 <= it->GetTo() ) {
TSeqPos cut_mrna_len = ( 3 - ( p2 - it->GetFrom()) % 3 ) %3, cnt = 0;
string transcript = segments[pos2].m_details;
int i = 0;
for( ; i < (int)transcript.size(); ++i) {
if( cnt%3 == cut_mrna_len && transcript[i] == 'M' ) { //cut point
CutFromLeft(i, segments[pos2]);
break;
}
if( transcript[i] != 'I' ) ++cnt;
}
if( i == (int)transcript.size() ) {// exon should not be so bad
NCBI_THROW(CAlgoAlignException, eInternal, g_msg_InvalidRange);
}
break;
}
}
}
}
AdjustGaps(segments);
}
