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/*******************************************************************************
* $Id: ClustalInterface.h,v 1.12 2004/04/19 23:10:50 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 _ClustalInterface_h_
#define _ClustalInterface_h_
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libMems/NumericMatrix.h"
#include "libGenome/gnFilter.h"
#include "libGenome/gnSequence.h"
#include "libMems/GappedAlignment.h"
#include "libMems/GappedAligner.h"
// attempt to auto-link the ClustalW library on windows
#if defined(WIN64)&&defined(NDEBUG)&&!defined(FASTDEBUG)&&defined(_OPENMP)
#pragma comment(lib, "ClustalW64omp.lib")
#endif
#if defined(WIN64)&&defined(FASTDEBUG)&&defined(_OPENMP)
#pragma comment(lib, "ClustalW64fdomp.lib")
#endif
#if defined(WIN32)&&!defined(WIN64)&&defined(NDEBUG)&&!defined(FASTDEBUG)&&defined(_OPENMP)
#pragma comment(lib, "ClustalWomp.lib")
#endif
#if defined(WIN32)&&!defined(WIN64)&&defined(FASTDEBUG)&&defined(_OPENMP)
#pragma comment(lib, "ClustalWfdomp.lib")
#endif
#if defined(WIN64)&&defined(NDEBUG)&&!defined(FASTDEBUG)&&!defined(_OPENMP)
#pragma comment(lib, "ClustalW64.lib")
#endif
#if defined(WIN64)&&defined(FASTDEBUG)&&!defined(_OPENMP)
#pragma comment(lib, "ClustalW64fd.lib")
#endif
#if defined(WIN32)&&!defined(WIN64)&&defined(NDEBUG)&&!defined(FASTDEBUG)&&!defined(_OPENMP)
#pragma comment(lib, "ClustalW.lib")
#endif
#if defined(WIN32)&&!defined(WIN64)&&defined(FASTDEBUG)&&!defined(_OPENMP)
#pragma comment(lib, "ClustalWfd.lib")
#endif
namespace mems {
class ClustalInterface : public GappedAligner {
public:
/**
* Returns a reference to a usable ClustalInterface
*/
static ClustalInterface& getClustalInterface();
/**
* Attempts to perform a multiple alignment using ClustalW between
* <code>r_begin</code> and <code>r_end</code>
*/
boolean Align( GappedAlignment& cr, Match* r_begin, Match* r_end, std::vector< genome::gnSequence* >& seq_table );
/**
* Set the distance matrix to use when computing alignments, writes the guide tree to the location
* specified in <code>tree_filename</code>
* @param distance_matrix An NxN distance matrix for the sequences
* @param tree_filename The output file name for the guide tree
*/
void SetDistanceMatrix( NumericMatrix< double >& distance_matrix, std::string& tree_filename );
/**
* Set the minimum flank size used to anchor alignments on the sequences
*/
void SetMinFlankSize( gnSeqI min_flank ){ min_flank_size = min_flank; }
/**
* Try using the guide tree in the file given by tree_filename. Throws an
* exception if the tree file couldn't be loaded
* @param tree_filename The path to the guide tree file
* @param dist_mat The distance matrix relating sequences
* @param seq_count The number of genomes in the guide tree file
*/
void setGuideTree( std::string& tree_filename, NumericMatrix< double >& dist_mat, uint seq_count );
/** returns true if a guide tree has been loaded already */
boolean guideTreeLoaded() const { return distance_matrix.cols() > 0; };
void SetDistanceMatrix( NumericMatrix< double >& distance_matrix, std::string& tree_filename, boolean reread_tree );
protected:
boolean CallClustal( std::vector< std::string >& seq_table );
NumericMatrix< double > distance_matrix;
gnSeqI min_flank_size;
int clustal_score_cutoff;
bool allocated_aln;
private:
ClustalInterface( const ClustalInterface& ci ){ *this = ci; }
ClustalInterface& operator=( const ClustalInterface& ci );
ClustalInterface();
};
}
#endif // _ClustalInterface_h_
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