d3/d9b/_bio_gene_prediction_8h_source.html

00001 #ifndef BIOGENEPREDICTION_H
00002 #define BIOGENEPREDICTION_H
00003
00004 #include "BioDnaSequence.h"
00005 #include "BioFasta.h"
00006 #include "BioRaw.h"
00007 #include "BioWordHit.h"
00008 #include "BioUtilities.h"
00009 #include "BioGenBank.h"
00010 #include "BioEmbl.h"
00011
00012 class BioGenePrediction
00013 {
00014   private:
00015   string seqPredict_;
00016   vector< vector<BioWordHit> > frames_;
00017   bool ORFSFOUND;
00018   void findORFs();
00019   void calculateORFs(const string&,int);
00020   void calculateReverseORFs(const string&);
00021
00022   public:
00023
00024   BioGenePrediction(){}
00025   BioGenePrediction(BioDnaSequence& BioDnaSequenceObject );
00026   BioGenePrediction(BioGenBank& GenBankObject );
00027   BioGenePrediction(BioEmbl& EmblObject );
00028   BioGenePrediction(BioFasta& BioFastaObject );
00029   BioGenePrediction(BioRaw& );
00030
00031   long getNumberOfOrfs(int frameNum);
00032   vector<BioSequence> getOrfs(int frameNum);
00033   long getNumberOfOrfs(int frameNum,int minSequenceLength,int maxSequenceLength = 0);
00034   vector<BioSequence> getOrfs(int frameNum,int minSequenceLength,int maxSequenceLength = 0);
00035   void showTATABoxes();
00036
00037   void showOrfs(int frameNum, ostream& os = cout);
00038   void showOrfs(int frameNum,int minSequenceLength,int maxSequenceLength = 0, ostream& os = cout);
00039 };
00040
00041 #endif