CRef<CSeq_entry>
CShortReadFastaInputSource::x_ReadFastaOneSeq(CRef<ILineReader> line_reader)
{
int start = 0;
// parse the last read defline
CTempString line = **line_reader;
CTempString id = x_ParseDefline(line);
CRef<CSeq_id> seqid(new CSeq_id);
seqid->Set(CSeq_id::e_Local, id);
++(*line_reader);
line = **line_reader;
while (line[0] != '>') {
// ignore empty lines
if (line.empty() && !line_reader->AtEOF()) {
++(*line_reader);
line = **line_reader;
continue;
}
// copy the sequence
// increase the sequence buffer if necessary
if (start + line.length() + 1 > m_SeqBuffLen) {
string tmp;
m_SeqBuffLen = 2 * (start + line.length() + 1);
tmp.reserve(m_SeqBuffLen);
memcpy(&tmp[0], &m_Sequence[0], start);
m_Sequence.swap(tmp);
}
memcpy(&m_Sequence[start], line.data(), line.length());
start += line.length();
if (line_reader->AtEOF()) {
break;
}
// read next line
++(*line_reader);
line = **line_reader;
}
// set up sequence
if (start > 0) {
CRef<CSeq_entry> seq_entry(new CSeq_entry);
CBioseq& bioseq = seq_entry->SetSeq();
bioseq.SetInst().SetMol(CSeq_inst::eMol_na);
bioseq.SetInst().SetRepr(CSeq_inst::eRepr_raw);
bioseq.SetId().clear();
bioseq.SetId().push_back(seqid);
bioseq.SetInst().SetLength(start);
m_Sequence[start] = 0;
bioseq.SetInst().SetSeq_data().SetIupacna(CIUPACna(&m_Sequence[0]));
bioseq.SetDescr();
m_BasesAdded += start;
return seq_entry;
}
return CRef<CSeq_entry>();
}
static CProt_ref::EECNumberFileStatus s_LoadECNumberTable(const string& dir, const string& name,
const char* const *fallback,
size_t fallback_count,
CProt_ref::EECNumberStatus status)
{
CRef<ILineReader> lr;
CProt_ref::EECNumberFileStatus rval = CProt_ref::eECFile_not_attempted;
if ( !dir.empty() ) {
lr.Reset(ILineReader::New
(CDirEntry::MakePath(dir, "ecnum_" + name, "txt")));
rval = CProt_ref::eECFile_not_found;
}
if (lr.Empty()) {
while (fallback_count--) {
s_ProcessECNumberLine(*fallback++, status);
}
} else {
rval = CProt_ref::eECFile_not_read;
do {
s_ProcessECNumberLine(*++*lr, status);
rval = CProt_ref::eECFile_read;
} while ( !lr->AtEOF() );
}
return rval;
}
static void s_LoadECNumberTable(const string& dir, const string& name,
const char* const *fallback,
size_t fallback_count,
CProt_ref::EECNumberStatus status)
{
CRef<ILineReader> lr;
if ( !dir.empty() ) {
lr.Reset(ILineReader::New
(CDirEntry::MakePath(dir, "ecnum_" + name, "txt")));
}
if (lr.Empty()) {
while (fallback_count--) {
s_ProcessECNumberLine(*fallback++, status);
}
} else {
do {
s_ProcessECNumberLine(*++*lr, status);
} while ( !lr->AtEOF() );
}
}
CRef<CSeq_entry>
CShortReadFastaInputSource::x_ReadFastqOneSeq(CRef<ILineReader> line_reader)
{
CTempString line;
CTempString id;
CRef<CSeq_entry> retval;
// first read defline
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
if (line[0] != '@') {
NCBI_THROW(CInputException, eInvalidInput, (string)"FASTQ parse error:"
" defline expected at line: " +
NStr::IntToString(line_reader->GetLineNumber()));
}
id = x_ParseDefline(line);
CRef<CSeq_id> seqid(new CSeq_id);
seqid->Set(CSeq_id::e_Local, id);
// read sequence
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
// set up sequence
if (line.length() > 0) {
CRef<CSeq_entry> seq_entry(new CSeq_entry);
CBioseq& bioseq = seq_entry->SetSeq();
bioseq.SetInst().SetMol(CSeq_inst::eMol_na);
bioseq.SetInst().SetRepr(CSeq_inst::eRepr_raw);
bioseq.SetId().clear();
bioseq.SetId().push_back(seqid);
bioseq.SetInst().SetLength(line.length());
bioseq.SetInst().SetSeq_data().SetIupacna(CIUPACna(line.data()));
bioseq.SetDescr();
m_BasesAdded += line.length();
retval = seq_entry;
}
// read and skip second defline
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
if (line[0] != '+') {
NCBI_THROW(CInputException, eInvalidInput, (string)"FASTQ parse error:"
" defline expected at line: " +
NStr::IntToString(line_reader->GetLineNumber()));
}
// read and skip quality scores
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
return retval;
}