d3/ddf/_bio_single_blast_8h_source.html

00001 /****************************************************************************
00002 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
00003 The BioBhasha : The Biologist's Programming Language
00004 Version 1.0 (19th December 2001)
00005 Prasad, B.V.L.S.
00006 Contact: burrashiva@yahoo.com
00007 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
00008 *****************************************************************************/
00009 #ifndef BIOSINGLEBLAST_H
00010 #define BIOSINGLEBLAST_H
00011
00012 #include "BioUtilities.h"
00013
00014 class BioSingleBlast
00015 {
00016         friend bool operator < ( const BioSingleBlast& x, const BioSingleBlast& y);
00017         friend bool operator > ( const BioSingleBlast& x, const BioSingleBlast& y);
00018         friend bool operator == ( const BioSingleBlast& x, const BioSingleBlast& y);
00019
00020         string seqName_;
00021         float score_;
00022         double eValue_;
00023         int positives_;
00024         int identities_;
00025         int  gaps_;
00026         int alignedFragmentLength_;
00027         int length_;
00028
00029         vector <string> alignment_;
00030         public:
00031
00032         BioSingleBlast( vector <string> oneBlast );
00033         string getSequenceName();
00034         int getSequenceLength();
00035         int getAlignedFragmentLength();
00036         int getNumberOfIdentities();
00037         int getNumberOfGaps();
00038         int getNumberOfPositives();
00039         float getScore();
00040         double getEValue();
00041         void showAlignment(ostream& os = cout);
00042         vector<string> getAlignment();
00043
00044 };
00045
00046 #endif