d2/de6/_bio_protein_sequence_dot_plot_8h_source.html

00001 #ifndef BIOPROTEINSEQUENCEDOTPLOT_H
00002 #define BIOPROTEINSEQUENCEDOTPLOT_H
00003
00004 #include "BioProteinSequence.h"
00005 #include "BioProteinSubstitutionMatrix.h"
00006 #include "BioLenPos.h"
00007 #include "BioSwissProt.h"
00008 #include "BioFasta.h"
00009 #include "BioPostScript.h"
00010
00011 class BioProteinSequenceDotPlot
00012 {
00013   private :
00014                  string seq1;
00015                  string seq2;
00016                  string nameSeq1_;
00017                  string nameSeq2_;
00018                  string graphLabel_;
00019
00020                  float r_,g_,b_;
00021                  unsigned int windowSize_,stringency_;
00022
00023 //                 void ParseMatrix();
00024                  int compare(string str1,string str2,unsigned int s);
00025
00026   public  :
00027     BioProteinSequenceDotPlot(){}
00028
00029     BioProteinSequenceDotPlot(BioProteinSequence,BioProteinSequence,string="IDENTITY");
00030     BioProteinSequenceDotPlot(BioProteinSequence,string,string="IDENTITY");
00031
00032     BioProteinSequenceDotPlot(BioSwissProt,BioSwissProt,string="IDENTITY");
00033     BioProteinSequenceDotPlot(BioSwissProt,string,string="IDENTITY");
00034
00035     BioProteinSequenceDotPlot(BioFasta,BioFasta,string="IDENTITY");
00036     BioProteinSequenceDotPlot(BioFasta,string,string="IDENTITY");
00037
00038     BioProteinSequenceDotPlot(string,string,string="IDENTITY");
00039
00040     void showDotPlot(BioPostScript& ps,unsigned int startX_=80,unsigned int startY_=200,unsigned int size_=500);
00041     void setPlotColor(unsigned int r,unsigned int g, unsigned int b);
00042     void setLabels (string,string,string);
00043     void setWindowSize(unsigned int windowSize);
00044     void setStringency(unsigned int stringency);
00045
00046 };
00047
00048 #endif