///////////////////////////////////////////////////////
///
/// Read a string from a stream. The string is following
/// by its size
///
inline string ReadStringFromStream(CNcbiIstream& is)
{
string str;
if (!is.good() || is.eof())
return str;
size_t size;
is >> size;
if (!is.good() || is.eof())
return str;
vector<char> buf(size+1, 0);
is.read(&*buf.begin(), size+1);
size_t count = is.gcount();
if (count > 0)
str.append((&*buf.begin())+1, count-1);
return str;
}
/**
**\brief Object constructor.
**
**\param newInputStream input stream to read data from.
**\param is_nucl true if the input is DNA, false if it is protein
**\param parse_seqids false to disable parsing of deflines
**
**/
CMaskFastaReader( CNcbiIstream & newInputStream, bool is_nucl = true,
bool parse_seqids = false )
: CMaskReader( newInputStream ), is_nucleotide_(is_nucl),
parse_seqids_(parse_seqids),
fasta_reader_( newInputStream,
CONST_FLAGS |
(is_nucl ? objects::CFastaReader::fAssumeNuc
: objects::CFastaReader::fAssumeProt) |
(parse_seqids ? 0
: objects::CFastaReader::fNoParseID) )
{
if( !newInputStream && !newInputStream.eof() ) {
NCBI_THROW( Exception, eBadStream,
"bad stream state at fasta mask reader initialization" );
}
}
// Helper function for loading alignments. Returns number of alignments loaded
// into the container. The expected format is:
// <int-number-of-alignments>
// <Seq-align>+
size_t LoadAligns(CNcbiIstream& in,
CAlnContainer& aligns,
size_t limit = 0)
{
size_t num_aligns = 0;
while ( !in.eof() ) {
try {
CRef<CSeq_align> align(new CSeq_align);
in >> MSerial_AsnText >> *align;
align->Validate(true);
aligns.insert(*align);
num_aligns++;
if (limit > 0 && num_aligns >= limit) break;
}
catch (CIOException e) {
break;
}
}
return num_aligns;
}
// ----------------------------------------------------------------------------
void CMultiReaderApp::xProcessNewick(
const CArgs& args,
CNcbiIstream& istr,
CNcbiOstream& ostr)
// ----------------------------------------------------------------------------
{
string strTree;
char c = istr.get();
while (!istr.eof()) {
strTree += c;
if (c == ';') {
CNcbiIstrstream istrstr(strTree.c_str());
auto_ptr<TPhyTreeNode> pTree(ReadNewickTree(istrstr) );
CRef<CBioTreeContainer> btc = MakeBioTreeContainer(pTree.get());
xWriteObject(*btc, ostr);
strTree.clear();
}
c = istr.get();
}
}