/usr/include/libMems-1.6/libMems/IntervalList.h is in libmems-1.6-dev 1.6.0+4725-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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* $Id: GenericIntervalList.h,v 1.6 2004/03/01 02:40:08 darling Exp $
* This file is copyright 2002-2007 Aaron Darling and authors listed in the AUTHORS file.
* This file is licensed under the GPL.
* Please see the file called COPYING for licensing details.
* **************
******************************************************************************/
#ifndef _IntervalList_h_
#define _IntervalList_h_
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <iostream>
#include <list>
#include <sstream>
#include "libMems/SortedMerList.h"
#include "libGenome/gnSequence.h"
#include "libMems/Interval.h"
#include "libMems/MemHash.h"
#include "libMems/CompactGappedAlignment.h"
#include "libGenome/gnSourceFactory.h"
#include "libGenome/gnFASSource.h"
#include "libGenome/gnSEQSource.h"
#include "libGenome/gnGBKSource.h"
#include "libGenome/gnRAWSource.h"
namespace mems {
/**
* This class represents a set Intervals, each of which is a collinear aligned region
* There are functions to read and write an GenericIntervalList.
* @see Interval
*/
template< class MatchType = Interval >
class GenericIntervalList : public std::vector< MatchType > {
public:
GenericIntervalList(){};
GenericIntervalList( const GenericIntervalList& ml );
GenericIntervalList& operator=( const GenericIntervalList& ml );
/**
* Deletes the objects associated
* with this GenericIntervalList.
*/
void Clear();
/**
* Reads a GenericIntervalList from an input stream
* Sequence and SML file names are read into the seq_filename
* and sml_filename vectors, but the actual files are not
* opened. The calling function should load them after
* using this method.
* @param match_stream The input stream to read from
*/
void ReadList( std::istream& match_stream );
/**
* Writes a GenericIntervalList to the designated output stream
* @param match_stream The outptu stream to write to
*/
void WriteList( std::ostream& match_stream ) const;
/**
* Writes a gapped alignment of sequences to the output stream
*/
void WriteAlignedSequences(std::ostream& match_file) const;
/**
* Writes a gapped alignment of sequences in a standard format
*/
void WriteStandardAlignment( std::ostream& out_file ) const;
/**
* Writes a gapped alignment of sequences in xml format
*/
void WriteXMLAlignment( std::ostream& out_file ) const;
/**
* Reads in a set of intervals that are in xmfa (eXtended MultiFastA) format
*/
void ReadStandardAlignment( std::istream& in_stream );
/**
* Reads in a set of intervals that are in xmfa (eXtended MultiFastA) format
* and stores them in CompactGappedAlignments<>
*/
void ReadStandardAlignmentCompact( std::istream& in_stream );
std::vector<std::string> seq_filename; /**< The names of files associated with the sequences used by this alignment */
std::vector<genome::gnSequence*> seq_table; /**< The actual sequences used in this alignment */
std::string backbone_filename; /**< The name of an associated backbone file, or empty if none exists */
protected:
};
typedef GenericIntervalList<> IntervalList;
template< class MatchType >
GenericIntervalList<MatchType>::GenericIntervalList( const GenericIntervalList<MatchType>& ml )
{
*this = ml;
}
template< class MatchType >
GenericIntervalList<MatchType>& GenericIntervalList<MatchType>::operator=( const GenericIntervalList<MatchType>& ml )
{
std::vector< MatchType >::operator=( ml );
seq_filename = ml.seq_filename;
seq_table = ml.seq_table;
return *this;
}
template< class MatchType >
void GenericIntervalList<MatchType>::Clear()
{
for( uint seqI = 0; seqI < seq_table.size(); seqI++ ){
if( seq_table[ seqI ] != NULL )
delete seq_table[ seqI ];
}
seq_filename.clear();
this->clear();
}
template< class MatchType >
void GenericIntervalList<MatchType>::ReadList(std::istream& match_file)
{
std::string tag;
gnSeqI len;
int64 start;
unsigned int seq_count;
uint seqI;
match_file >> tag; //format version tag
if( tag != "FormatVersion" ){
Throw_gnEx(InvalidFileFormat());
}
match_file >> tag; //format version
if( tag != "4" ){
Throw_gnEx(InvalidFileFormat());
}
match_file >> tag; //sequence count tag
if( tag != "SequenceCount" ){
Throw_gnEx(InvalidFileFormat());
}
match_file >> seq_count; //sequence count
if(seq_count < 2){
Throw_gnEx(InvalidFileFormat());
}
std::vector< std::string > alignment;
// read the sequence file names and lengths
for( seqI = 0; seqI < seq_count; seqI++ ){
match_file >> tag; // name tag
getline( match_file, tag );
// skip the tab character
tag = tag.substr( 1 );
seq_filename.push_back(tag);
// try{
// gnSequence *new_seq = new gnSequence();
// new_seq->LoadSource(tag);
// seq_table.push_back( new_seq );
// }catch( gnException& gne );
match_file >> tag; // length tag
match_file >> tag; // length
alignment.push_back( "" ); // initialize alignment vector
}
uint interval_count;
match_file >> tag; // interval count tag
match_file >> interval_count; // interval count
// read the matches
std::string cur_line;
Interval* cur_iv = NULL;
boolean clustal_match;
std::vector< AbstractMatch* > iv_matches;
bool parsing = false;
while( std::getline( match_file, cur_line ) ){
if( cur_line.find( "Interval" ) != std::string::npos ){
// end the old interval
if( iv_matches.size() > 0 )
{
this->push_back( Interval(iv_matches.begin(), iv_matches.end()) );
// for( size_t mI = 0; mI < iv_matches.size(); mI++ )
// delete iv_matches[mI];
iv_matches.clear();
}
parsing = true;
continue;
}
if( !parsing )
continue;
if( cur_line.length() == 0 )
continue;
clustal_match = false;
if( cur_line == "GappedAlignment" ){
clustal_match = true;
getline( match_file, cur_line );
std::stringstream line_stream( cur_line );
line_stream >> len;
GappedAlignment* cr = new GappedAlignment( seq_count, len );
for( seqI = 0; seqI < seq_count; seqI++ ){
line_stream >> start;
cr->SetStart( seqI, start );
std::getline( match_file, alignment[ seqI ] );
int64 seq_len = 0;
for( uint charI = 0; charI < alignment[ seqI ].length(); charI++ )
if( alignment[ seqI ][ charI ] != '-' )
seq_len++;
cr->SetLength( seq_len, seqI );
}
cr->SetAlignment( alignment );
iv_matches.push_back( cr );
}
else{
Match mmhe( seq_count );
Match* mhe = mmhe.Copy();
std::stringstream line_stream( cur_line );
line_stream >> len;
mhe->SetLength(len);
for( seqI = 0; seqI < seq_count; seqI++){
line_stream >> start;
mhe->SetStart(seqI, start);
}
iv_matches.push_back( mhe );
}
}
if( iv_matches.size() > 0 )
this->push_back( Interval(iv_matches.begin(), iv_matches.end()) );
if( interval_count != this->size() ){
Throw_gnEx(InvalidFileFormat());
}
}
template< class MatchType >
void GenericIntervalList<MatchType>::WriteList(std::ostream& match_file) const
{
unsigned int seq_count = seq_table.size();
uint seqI;
match_file << "FormatVersion" << '\t' << 4 << "\n";
match_file << "SequenceCount" << '\t' << seq_count << "\n";
for(seqI = 0; seqI < seq_count; seqI++){
match_file << "Sequence" << seqI << "File" << '\t';
if( seq_filename.size() > seqI )
match_file << seq_filename[seqI];
else
match_file << "null";
match_file << "\n";
match_file << "Sequence" << seqI << "Length" << '\t';
if( seq_table.size() > seqI )
match_file << seq_table[seqI]->length();
else
match_file << "0";
match_file << "\n";
}
match_file << "IntervalCount" << '\t' << this->size() << std::endl;
for( uint ivI = 0; ivI < this->size(); ivI++ ){
match_file << "Interval " << ivI << std::endl;
const std::vector<AbstractMatch*>& matches = (*this)[ ivI ].GetMatches();
for( uint matchI = 0; matchI < matches.size(); matchI++ ){
const AbstractMatch* m = matches[ matchI ];
const GappedAlignment* cr = dynamic_cast< const GappedAlignment* >( m );
const Match* match = dynamic_cast< const Match* >( m );
if( match != NULL ){
match_file << *match << std::endl;
}
else if( cr != NULL ){
match_file << "GappedAlignment\n";
match_file << cr->Length();
for( seqI = 0; seqI < seq_count; seqI++ )
match_file << '\t' << cr->Start( seqI );
match_file << std::endl;
const std::vector< std::string >& align_matrix = GetAlignment( *cr, seq_table );
for( seqI = 0; seqI < seq_count; seqI++ )
match_file << align_matrix[ seqI ] << std::endl;
}
}
match_file << std::endl;
}
}
//stub for now, later use a XML library to write/read alignments in xml format..
template< class MatchType >
void GenericIntervalList<MatchType>::WriteXMLAlignment( std::ostream& out_file ) const
{
if( this->size() == 0 )
return;
// write source sequence filenames and formats
// to make Paul happy
boolean single_input = true;
uint seqI = 0;
for( seqI = 1; seqI < seq_filename.size(); seqI++ ){
if( seq_filename[ 0 ] != seq_filename[ seqI ] ){
single_input = false;
break;
}
}
// unsigned int seq_count = seq_table.size();
out_file << "<procrastAlignment sequence=\"" << seq_filename[ 0 ] << "\">" << std::endl;
for( uint ivI = 0; ivI < this->size(); ivI++ ){
if( (*this)[ ivI ].AlignmentLength() == 0 ){
continue;
}
out_file << "\t<localAlignment id = \"" << ivI+1 << "\" length = \"" << (*this)[ ivI ].AlignmentLength() << "\" multiplicity = \"" << (*this)[ ivI ].Multiplicity() << "\" spscore=\"" << (*this)[ ivI ].spscore << "\">" << std::endl;
std::vector<std::string> alignment;
if( seq_table.size() == 1 && seq_table.size() != (*this)[ ivI ].SeqCount() )
{
GetAlignment( (*this)[ ivI ], std::vector<genome::gnSequence*>((*this)[ ivI ].SeqCount(), seq_table[0]), alignment );
}else
GetAlignment( (*this)[ ivI ], seq_table, alignment );
for( seqI = 0; seqI < (*this)[ ivI ].SeqCount(); seqI++ ){
int64 startI = (*this)[ ivI ].Start( seqI );
gnSeqI length = (*this)[ ivI ].Length( seqI );
// if this genome doesn't have any sequence in this
// interval then skip it...
if( startI == 0 &&ivI > 0) // kludge: write all seqs into the first interval so java parser can read it
continue;
out_file << "\t\t<component id=\"" << seqI+1 << "\" seqid=\"1\" leftend=\"" << (*this)[ ivI ].LeftEnd( seqI ) << "\" length=\"" << (*this)[ ivI ].Length( seqI ) << "\" orientation=\"" << (*this)[ ivI ].Orientation( seqI) << "\">" << alignment[ seqI ].data();
out_file << "\t\t</component> " << std::endl;
}
out_file << "\t</localAlignment>" << std::endl;
}
out_file << "</procrastAlignment>" << std::endl;
}
template< class MatchType >
void GenericIntervalList<MatchType>::WriteStandardAlignment( std::ostream& out_file ) const
{
if( this->size() == 0 )
return;
// unsigned int seq_count = seq_table.size();
uint seqI = 0;
// write out the format version
out_file << "#FormatVersion Mauve1" << std::endl;
// write source sequence filenames and formats
// to make Paul happy
boolean single_input = true;
for( seqI = 1; seqI < seq_filename.size(); seqI++ ){
if( seq_filename[ 0 ] != seq_filename[ seqI ] ){
single_input = false;
break;
}
}
for( seqI = 0; seqI < seq_filename.size(); seqI++ ){
out_file << "#Sequence" << seqI + 1 << "File\t" << seq_filename[ seqI ] << std::endl;
if( single_input )
out_file << "#Sequence" << seqI + 1 << "Entry\t" << seqI + 1 << std::endl;
genome::gnSourceFactory* sf = genome::gnSourceFactory::GetSourceFactory();
genome::gnBaseSource* gnbs = sf->MatchSourceClass( seq_filename[ seqI ] );
genome::gnFASSource* gnfs = dynamic_cast< genome::gnFASSource* >(gnbs);
genome::gnRAWSource* gnrs = dynamic_cast< genome::gnRAWSource* >(gnbs);
genome::gnSEQSource* gnss = dynamic_cast< genome::gnSEQSource* >(gnbs);
genome::gnGBKSource* gngs = dynamic_cast< genome::gnGBKSource* >(gnbs);
if( gnfs != NULL )
out_file << "#Sequence" << seqI + 1 << "Format\tFastA" << std::endl;
else if( gnrs != NULL )
out_file << "#Sequence" << seqI + 1 << "Format\traw" << std::endl;
else if( gnss != NULL ){
out_file << "#Sequence" << seqI + 1 << "Format\tDNAstar" << std::endl;
out_file << "#Annotation" << seqI + 1 << "File\t" << seq_filename[ seqI ] << std::endl;
out_file << "#Annotation" << seqI + 1 << "Format\tDNAstar" << std::endl;
}else if( gngs != NULL ){
out_file << "#Sequence" << seqI + 1 << "Format\tGenBank" << std::endl;
out_file << "#Annotation" << seqI + 1 << "File\t" << seq_filename[ seqI ] << std::endl;
out_file << "#Annotation" << seqI + 1 << "Format\tGenBank" << std::endl;
}
}
if( this->backbone_filename != "" )
out_file << "#BackboneFile\t" << this->backbone_filename << std::endl;
for( uint ivI = 0; ivI < this->size(); ivI++ ){
if( (*this)[ ivI ].AlignmentLength() == 0 ){
continue;
}
std::vector<std::string> alignment;
if( seq_table.size() == 1 && seq_table.size() != (*this)[ ivI ].SeqCount() )
{
GetAlignment( (*this)[ ivI ], std::vector<genome::gnSequence*>((*this)[ ivI ].SeqCount(), seq_table[0]), alignment );
}else
GetAlignment( (*this)[ ivI ], seq_table, alignment );
for( seqI = 0; seqI < (*this)[ ivI ].SeqCount(); seqI++ ){
int64 startI = (*this)[ ivI ].Start( seqI );
gnSeqI length = (*this)[ ivI ].Length( seqI );
// if this genome doesn't have any sequence in this
// interval then skip it...
if( startI == 0 &&ivI > 0) // kludge: write all seqs into the first interval so java parser can read it
continue;
out_file << "> " << seqI + 1 << ":";
if( startI > 0 ){
out_file << genome::absolut( startI ) << "-" << genome::absolut( startI ) + length - 1 << " + ";
}else if(startI == 0){
out_file << 0 << "-" << 0 << " + ";
}else{
out_file << genome::absolut( startI ) << "-" << genome::absolut( startI ) + length - 1 << " - ";
}
if( single_input )
out_file << seq_filename[ 0 ]; // write the sequence filename as the seq name
else
out_file << seq_filename[ seqI ]; // write the sequence filename as the seq name
out_file << std::endl;
gnSeqI cur_pos = 0;
for( ; cur_pos < alignment[ seqI ].length(); cur_pos += 80 ){
gnSeqI cur_len = cur_pos + 80 < alignment[ seqI ].length() ? 80 : alignment[ seqI ].length() - cur_pos;
out_file.write( alignment[ seqI ].data() + cur_pos, cur_len );
out_file << std::endl;
}
}
out_file << "=" << std::endl;
out_file.flush();
}
}
template< class MatchType >
void GenericIntervalList<MatchType>::ReadStandardAlignment( std::istream& in_stream )
{
uint seq_count = 0;
gnSeqI max_len = 0;
std::string cur_line;
if( !std::getline( in_stream, cur_line ) )
{
Clear(); // if we can't read from the file then just return an empty interval list
return;
}
uint seqI = 0;
std::vector< gnSeqI > lengths;
std::vector< GappedAlignment* > ga_list;
GappedAlignment cr;
std::string empty_line;
std::vector< std::string > aln_mat;
uint line_count = 1;
while( true ){
while( cur_line[0] == '#' ){
// hit a comment or metadata. try to parse it if it's a filename
std::getline( in_stream, cur_line );
line_count++;
std::stringstream ss( cur_line );
std::string token;
std::getline( ss, token, '\t' );
if( token.substr(1, 8) != "Sequence" || token.find( "File" ) == std::string::npos )
continue;
std::getline( ss, token );
seq_filename.push_back( token );
}
// read and parse the def. line
std::stringstream line_str( cur_line );
std::getline( line_str, cur_line, '>' );
std::getline( line_str, cur_line, ':' );
// take off leading whitespace
std::stringstream parse_str( cur_line );
parse_str >> seqI; // the sequence number
int64 start, stop;
std::getline( line_str, cur_line, '-' );
parse_str.clear();
parse_str.str( cur_line );
parse_str >> start;
line_str >> stop;
std::string strand;
line_str >> strand;
std::string name; // anything left is the name
std::getline( line_str, name );
// read and parse the sequence
while( aln_mat.size() < seqI )
aln_mat.push_back( empty_line );
gnSeqI chars = 0;
while( std::getline( in_stream, cur_line ) ){
line_count++;
if( (cur_line[ 0 ] == '>' ) || (cur_line[ 0 ] == '=' ))
break;
for( uint charI = 0; charI < cur_line.length(); charI++ )
if( cur_line[ charI ] != '-' )
chars++;
aln_mat[ seqI - 1 ] += cur_line;
}
while( lengths.size() < seqI )
lengths.push_back(0);
lengths[ seqI - 1 ] = chars;
// temporary workaround for file format inconsistency
if( strand == "+" )
cr.SetStart( seqI - 1, start );
else if( start < stop ){
if( chars == 0 )
cr.SetStart( seqI - 1, 0 );
else
cr.SetStart( seqI - 1, -start );
if( chars != stop - start + 1 && !(chars == 0 && stop - start == 1) ){
std::cerr << "Error in XMFA file format\n";
std::cerr << "Before line " << line_count << std::endl;
std::cerr << "Expecting " << stop - start + 1 << " characters based on defline\n";
std::cerr << "Actually read " << chars << " characters of sequence\n";
Throw_gnEx(InvalidFileFormat());
}
}else{
if( chars == 0 )
cr.SetStart( seqI - 1, 0 );
else
cr.SetStart( seqI - 1, -stop );
if( chars != start - stop + 1 && !(chars == 0 && stop - start == 1) ){
std::cerr << "Error in XMFA file format\n";
std::cerr << "Before line " << line_count << std::endl;
std::cerr << "Expecting " << start - stop + 1 << " characters based on defline\n";
std::cerr << "Actually read " << chars << " characters of sequence\n";
Throw_gnEx(InvalidFileFormat());
}
}
if( chars > max_len )
max_len = aln_mat[ seqI - 1 ].length();
if( cur_line.size() == 0 )
break;
// did we finish an aligned region?
if( cur_line[ 0 ] != '>' ){
GappedAlignment *new_cr = new GappedAlignment( aln_mat.size(), max_len );
for( uint seqJ = 0; seqJ < seqI; seqJ++ ){
new_cr->SetStart( seqJ, cr.Start( seqJ ) );
new_cr->SetLength( lengths[ seqJ ], seqJ );
cr.SetStart( seqJ, NO_MATCH );
}
for( uint seqJ = 0; seqJ < seqI; seqJ++ )
aln_mat[seqJ].resize( max_len, '-' );
new_cr->SetAlignment(aln_mat);
lengths.clear();
if( seq_count < seqI )
seq_count = seqI;
ga_list.push_back( new_cr );
max_len = 0; // reset length for the next interval
aln_mat.clear(); // reset cr for next interval
// bail out on EOF or corruption
if( cur_line[ 0 ] != '=' )
break;
// otherwise read up to the next def. line
while( std::getline( in_stream, cur_line ) ){
line_count++;
if( cur_line[ 0 ] == '>' )
break;
}
if( cur_line[ 0 ] != '>' )
break;
}
}
// now process all GappedAlignments into Intervals
for( uint ivI = 0; ivI < ga_list.size(); ivI++ ){
GappedAlignment* cr = ga_list[ ivI ];
GappedAlignment* new_cr = new GappedAlignment( seq_count, cr->AlignmentLength() );
const std::vector< std::string >& align_matrix = GetAlignment( *cr, seq_table );
std::vector< std::string > new_aln_mat(seq_count);
for( seqI = 0; seqI < align_matrix.size(); seqI++ ){
new_cr->SetLength( cr->Length( seqI ), seqI );
new_cr->SetStart( seqI, cr->Start(seqI) );
new_aln_mat[ seqI ] = align_matrix[ seqI ];
if( new_aln_mat[ seqI ].length() == 0 )
new_aln_mat[ seqI ] = std::string( new_cr->AlignmentLength(), '-' );
}
for( ; seqI < seq_count; seqI++ ){
new_cr->SetLength( 0, seqI );
new_cr->SetStart( seqI, 0 );
new_aln_mat[ seqI ] = std::string( new_cr->AlignmentLength(), '-' );
}
new_cr->SetAlignment(new_aln_mat);
delete cr;
cr = new_cr;
ga_list[ ivI ] = new_cr;
std::vector<AbstractMatch*> asdf(1, cr);
Interval iv( asdf.begin(), asdf.end() );
this->push_back( iv );
}
}
template< class MatchType >
void GenericIntervalList<MatchType>::ReadStandardAlignmentCompact( std::istream& in_stream )
{
uint seq_count = 0;
gnSeqI max_len = 0;
std::string cur_line;
std::getline( in_stream, cur_line );
uint seqI = 0;
std::vector< gnSeqI > lengths;
std::vector< GappedAlignment* > ga_list;
GappedAlignment cr;
std::string empty_line;
std::vector< std::string > aln_mat;
uint line_count = 1;
while( true ){
while( cur_line[0] == '#' ){
// hit a comment or metadata. try to parse it if it's a filename
std::getline( in_stream, cur_line );
line_count++;
std::stringstream ss( cur_line );
std::string token;
std::getline( ss, token, '\t' );
if( token.substr(1, 8) != "Sequence" || token.find( "File" ) == std::string::npos )
continue;
std::getline( ss, token );
seq_filename.push_back( token );
}
// read and parse the def. line
std::stringstream line_str( cur_line );
std::getline( line_str, cur_line, '>' );
std::getline( line_str, cur_line, ':' );
// take off leading whitespace
std::stringstream parse_str( cur_line );
parse_str >> seqI; // the sequence number
int64 start, stop;
std::getline( line_str, cur_line, '-' );
parse_str.clear();
parse_str.str( cur_line );
parse_str >> start;
line_str >> stop;
std::string strand;
line_str >> strand;
std::string name; // anything left is the name
std::getline( line_str, name );
// read and parse the sequence
while( aln_mat.size() < seqI )
aln_mat.push_back( empty_line );
gnSeqI chars = 0;
while( std::getline( in_stream, cur_line ) ){
line_count++;
if( (cur_line[ 0 ] == '>' ) || (cur_line[ 0 ] == '=' ))
break;
for( uint charI = 0; charI < cur_line.length(); charI++ )
if( cur_line[ charI ] != '-' )
chars++;
aln_mat[ seqI - 1 ] += cur_line;
}
while( lengths.size() < seqI )
lengths.push_back(0);
lengths[ seqI - 1 ] = chars;
// temporary workaround for file format inconsistency
if( strand == "+" )
cr.SetStart( seqI - 1, start );
else if( start < stop ){
if( chars == 0 )
cr.SetStart( seqI - 1, 0 );
else
cr.SetStart( seqI - 1, -start );
if( chars != stop - start + 1 && !(chars == 0 && stop - start == 1) ){
std::cerr << "Error in XMFA file format\n";
std::cerr << "Before line " << line_count << std::endl;
std::cerr << "Expecting " << stop - start + 1 << " characters based on defline\n";
std::cerr << "Actually read " << chars << " characters of sequence\n";
Throw_gnEx(InvalidFileFormat());
}
}else{
if( chars == 0 )
cr.SetStart( seqI - 1, 0 );
else
cr.SetStart( seqI - 1, -stop );
if( chars != start - stop + 1 && !(chars == 0 && stop - start == 1) ){
std::cerr << "Error in XMFA file format\n";
std::cerr << "Before line " << line_count << std::endl;
std::cerr << "Expecting " << start - stop + 1 << " characters based on defline\n";
std::cerr << "Actually read " << chars << " characters of sequence\n";
Throw_gnEx(InvalidFileFormat());
}
}
if( chars > max_len )
max_len = aln_mat[ seqI - 1 ].length();
if( cur_line.size() == 0 )
break;
// did we finish an aligned region?
if( cur_line[ 0 ] != '>' ){
GappedAlignment *new_cr = new GappedAlignment( aln_mat.size(), max_len );
for( uint seqJ = 0; seqJ < seqI; seqJ++ ){
new_cr->SetStart( seqJ, cr.Start( seqJ ) );
new_cr->SetLength( lengths[ seqJ ], seqJ );
cr.SetStart( seqJ, NO_MATCH );
}
for( uint seqJ = 0; seqJ < seqI; seqJ++ )
aln_mat[seqJ].resize( max_len, '-' );
new_cr->SetAlignment(aln_mat);
lengths.clear();
if( seq_count < seqI )
seq_count = seqI;
ga_list.push_back( new_cr );
max_len = 0; // reset length for the next interval
aln_mat.clear(); // reset cr for next interval
// bail out on EOF or corruption
if( cur_line[ 0 ] != '=' )
break;
// otherwise read up to the next def. line
while( std::getline( in_stream, cur_line ) ){
line_count++;
if( cur_line[ 0 ] == '>' )
break;
}
if( cur_line[ 0 ] != '>' )
break;
}
}
// now process all GappedAlignments into Intervals
//cerr << "Stuffing all GappedAlignments into Intervals" << endl;
for( uint ivI = 0; ivI < ga_list.size(); ivI++ )
{
GappedAlignment* cr = ga_list[ ivI ];
uint compact_seq_count = cr->SeqCount();
CompactGappedAlignment<>* new_cr = new CompactGappedAlignment<>(compact_seq_count, cr->AlignmentLength() );
const std::vector< std::string > align_matrix = GetAlignment( *cr, seq_table );
//cout << cr->SeqCount() << " " << seq_count << " " << align_matrix.size() << endl;
std::vector< std::string > new_aln_mat(compact_seq_count);
for( seqI = 0; seqI < compact_seq_count; seqI++ ){
new_cr->SetLength( cr->Length( seqI ), seqI );
new_cr->SetStart( seqI, cr->Start(seqI) );
new_aln_mat[ seqI ] = align_matrix[ seqI ];
if( new_aln_mat[ seqI ].length() == 0 )
new_aln_mat[ seqI ] = std::string( new_cr->AlignmentLength(), '-' );
}
for( ; seqI < compact_seq_count; seqI++ ){
new_cr->SetLength( 0, seqI );
new_cr->SetStart( seqI, 0 );
new_aln_mat[ seqI ] = std::string( new_cr->AlignmentLength(), '-' );
}
new_cr->SetAlignment( new_aln_mat );
delete cr;
//CompactGappedAlignment<>* cga = new_cr;
//ga_list[ ivI ] = dynamic_cast<GappedAlignment*>(cga);
Interval iv;
this->push_back( iv );
std::vector< AbstractMatch* > matches(1, new_cr);
this->back().SetMatches( matches );
}
}
template< class MatchType >
void GenericIntervalList<MatchType>::WriteAlignedSequences(std::ostream& match_file) const
{
unsigned int seq_count = seq_table.size();
uint seqI;
match_file << "mauveAligner data\n";
match_file << "FormatVersion" << '\t' << 5 << "\n";
match_file << "SequenceCount" << '\t' << seq_count << "\n";
for(seqI = 0; seqI < seq_count; seqI++){
match_file << "Sequence" << seqI << "File" << '\t';
if( seq_filename.size() > seqI )
match_file << seq_filename[seqI];
else
match_file << "null";
match_file << "\n";
match_file << "Sequence" << seqI << "Length" << '\t';
if( seq_table.size() > seqI )
match_file << seq_table[seqI]->length();
else
match_file << "0";
match_file << "\n";
}
match_file << "AlignmentCount" << '\t' << this->size() << std::endl;
if( this->size() == 0 )
return;
for( uint ivI = 0; ivI < this->size(); ivI++ ){
match_file << (*this)[ ivI ].AlignmentLength();
for( seqI = 0; seqI < seq_count; seqI++ )
match_file << '\t' << (*this)[ ivI ].Start( seqI );
match_file << std::endl;
std::vector<std::string> alignment;
GetAlignment( (*this)[ ivI ], this->seq_table, alignment );
for( seqI = 0; seqI < seq_count; seqI++ )
match_file << alignment[ seqI ] << std::endl;
match_file << std::endl;
}
}
}
#endif //_IntervalList_h_
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