// comparison function
bool CTextseq_id::Match(const CTextseq_id& tsip2) const
{
// Check Accessions first
if (IsSetAccession() && tsip2.IsSetAccession()) {
if ( PNocase().Equals(GetAccession(), tsip2.GetAccession()) ) {
if (IsSetVersion() && tsip2.IsSetVersion()) {
return GetVersion() == tsip2.GetVersion();
} else {
return true;
}
} else {
return false;
}
}
// then try name
if (IsSetName() && tsip2.IsSetName()) {
if ( PNocase().Equals(GetName(), tsip2.GetName()) ) {
if (IsSetVersion() && tsip2.IsSetVersion()) {
return GetVersion() == tsip2.GetVersion();
}
else {
return true;
}
} else {
return false;
}
}
//nothing to compare
return false;
}
// comparison function
int CTextseq_id::Compare(const CTextseq_id& tsip2) const
{
// Check Accessions first
// no-accession before accession
if ( int diff = IsSetAccession() - tsip2.IsSetAccession() ) {
return diff;
}
if ( IsSetAccession() ) {
_ASSERT(tsip2.IsSetAccession());
// sort by accession
if ( int diff = PNocase().Compare(GetAccession(),
tsip2.GetAccession()) ) {
return diff;
}
}
// Check version
// no-version before version
if ( int diff = IsSetVersion() - tsip2.IsSetVersion() ) {
return diff;
}
if ( IsSetVersion() ) {
_ASSERT(tsip2.IsSetVersion());
// smaller version first
if ( int diff = GetVersion() - tsip2.GetVersion() ) {
return diff;
}
}
if ( IsSetAccession() && IsSetVersion() ) {
// acc.ver are the same -> equal Seq-ids
return 0;
}
// Check name
// no-name before name
if ( int diff = IsSetName() - tsip2.IsSetName() ) {
return diff;
}
if ( IsSetName() ) {
_ASSERT(tsip2.IsSetName());
if ( int diff = PNocase().Compare(GetName(), tsip2.GetName()) ) {
return diff;
}
}
// All checks failed to distinguish Seq-ids.
return 0;
}
// format the contents FASTA string style
ostream& CTextseq_id::AsFastaString(ostream& s, bool allow_version) const
{
if (IsSetAccession()) {
s << GetAccession(); // no Upcase per Ostell - Karl 7/2001
if (allow_version && IsSetVersion()) {
int version = GetVersion();
if (version) {
s << '.' << version;
}
}
}
s << '|';
if ( IsSetName() ) {
s << GetName(); // no Upcase per Ostell - Karl 7/2001
}
return s;
}
CRef<CSeq_entry> CSraRun::GetSpotEntry(spotid_t spot_id) const
{
CRef<CSeq_entry> entry;
CSraStringValue name(m_Name, spot_id);
entry = new CSeq_entry();
CBioseq_set& seqset = entry->SetSet();
seqset.SetLevel(0);
seqset.SetClass(seqset.eClass_other);
CSraValueFor<SRASpotDesc> sdesc(m_SDesc, spot_id);
TSeqPos trim_start = m_Trim && m_TrimStart?
CSraValueFor<INSDC_coord_zero>(m_TrimStart, spot_id).Value(): 0;
TSeqPos trim_end = sdesc->clip_qual_right;
CSraValueFor<SRAReadDesc> rdesc(m_RDesc, spot_id);
CSraStringValue read(m_Read, spot_id);
CSraBytesValue qual(m_Qual, spot_id);
int seq_count = 0;
string id_start = GetAccession()+'.'+NStr::UIntToString(spot_id)+'.';
for ( int r = 0; r < sdesc->num_reads; ++r ) {
if ( rdesc[r].type != SRA_READ_TYPE_BIOLOGICAL ) {
continue;
}
TSeqPos len = rdesc[r].seg.len;
if ( len == 0 ) {
continue;
}
TSeqPos start = rdesc[r].seg.start;
TSeqPos end = start + len;
if ( m_Trim ) {
start = max(start, trim_start);
end = min(end, trim_end);
if ( start >= end ) {
continue;
}
len = end - start;
}
CRef<CSeq_entry> seq_entry(new CSeq_entry);
CBioseq& seq = seq_entry->SetSeq();
CRef<CSeq_id> id(new CSeq_id);
id->SetGeneral().SetDb("SRA");
id->SetGeneral().SetTag().SetStr(id_start+NStr::UIntToString(r+1));
seq.SetId().push_back(id);
{{
CRef<CSeqdesc> desc(new CSeqdesc);
desc->SetTitle(name.Value());
seq.SetDescr().Set().push_back(desc);
}}
{{
CSeq_inst& inst = seq.SetInst();
inst.SetRepr(inst.eRepr_raw);
inst.SetMol(inst.eMol_na);
inst.SetLength(len);
inst.SetSeq_data().SetIupacna().Set()
.assign(read.data()+start, len);
}}
{{
CRef<CSeq_annot> annot(new CSeq_annot);
CRef<CSeq_graph> graph(new CSeq_graph);
annot->SetData().SetGraph().push_back(graph);
graph->SetTitle("Phred Quality");
graph->SetLoc().SetWhole(*id);
graph->SetNumval(len);
CByte_graph& bytes = graph->SetGraph().SetByte();
bytes.SetAxis(0);
CByte_graph::TValues& values = bytes.SetValues();
values.reserve(len);
int min = kMax_Int;
int max = kMin_Int;
for ( size_t i = 0; i < len; ++i ) {
int v = qual[start+i];
values.push_back(v);
if ( v < min ) {
min = v;
}
if ( v > max ) {
max = v;
}
}
bytes.SetMin(min);
bytes.SetMax(max);
seq.SetAnnot().push_back(annot);
}}
seqset.SetSeq_set().push_back(seq_entry);
++seq_count;
}
switch ( seq_count ) {
case 0:
entry.Reset();
break;
case 1:
entry = seqset.GetSeq_set().front();
break;
}
return entry;
}
