src/org/gel/mauve/dcjx/DCJDistance.java

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package org.gel.mauve.dcjx;

import java.awt.CardLayout;
import java.awt.Panel;
import java.io.OutputStream;
import java.io.PrintStream;
import java.util.HashMap;
import java.util.Vector;

import javax.swing.JTextArea;

import org.gel.mauve.BaseViewerModel;
import org.gel.mauve.Genome;
import org.gel.mauve.XmfaViewerModel;
import org.gel.mauve.analysis.PermutationExporter;
import org.gel.mauve.gui.AnalysisDisplayWindow;

public class DCJDistance {

//      private JTextArea matrix;
        
        private static final String NWAY_COMMAND = "N-Way";
        private static final String NWAY_DESC = "Distances based on N-Way LCBs";
        private static final String PWISE_COMMAND = "Pairwise";
        private static final String PWISE_DESC = "Distances based on Pairwise LCBs";
        private static final String NBLKS_COMMAND = "NoBlocks";
        private static final String NBLKS_DESC = "Number of blocks between each pair";
        
        private static final String temp = "Running...";
        private static final String error = "Error computing DCJ distances! Please report bug to atritt@ucdavis.edu";
        
        private static HashMap<String,DCJDistance> modelMap;
        
        private JTextArea nwayTA, pwiseTA;
        
        private AnalysisDisplayWindow adw;
        
        private int fWIDTH = 400;

        private int fHEIGHT = 400;
        
        private DCJ[][] nWayDist;
        
        private DCJ[][] pWiseDist;
        
        private static DCJDistance curr;
        
        
//      private JTextArea log;
        // event listener
        
        public static void launchWindow(BaseViewerModel model) {
                if (modelMap == null)
                        modelMap = new HashMap<String,DCJDistance>();
                String key = model.getSrc().getAbsolutePath();
                if (modelMap.containsKey(key)) {        
                        modelMap.get(key).adw.showWindow();
                }else if (model instanceof XmfaViewerModel){
                        modelMap.put(key, new DCJDistance((XmfaViewerModel)model));
                } else {
                        System.err.println("Can't compute DCJ distance without contig boundaries.");
                }       
        }
        
        public DCJDistance (XmfaViewerModel model) {
                int numGenomes = model.getGenomes().size();
                // lets have some fun with interfaces
                DistanceFunction dcj = new DistanceFunction(){
                        public int distance(DCJ dcj) { return dcj.dcjDistance();}
                };
                DistanceFunction scj = new DistanceFunction(){
                        public int distance(DCJ dcj){ return dcj.scjDistance();}
                };
                DistanceFunction bp = new DistanceFunction(){
                        public int distance(DCJ dcj){ return dcj.bpDistance();}
                };
                if (numGenomes > 2){
                        adw = new AnalysisDisplayWindow("DCJ - "+model.getSrc().getName(), fWIDTH, fHEIGHT);
                        nwayTA = adw.addContentPanel(NWAY_COMMAND, NWAY_DESC, true);
                        pwiseTA = adw.addContentPanel(PWISE_COMMAND, PWISE_DESC, false);
                        adw.showWindow();
                        Vector<Genome> v = model.getGenomes();
                        Genome[] genomes = v.toArray(new Genome[v.size()]);
                        int numGen = genomes.length;
                        nWayDist = new DCJ[numGen][numGen];
                        pWiseDist = new DCJ[numGen][numGen];
                        nwayTA.append(temp);
                        pwiseTA.append(temp);
                        try {
                                loadMatrices(model, nWayDist, pWiseDist);
                                nwayTA.replaceRange("", 0, temp.length());
                                pwiseTA.replaceRange("", 0, temp.length());
                                nwayTA.append("# Rearrangement distances based on N-way LCBs\n");
                                nwayTA.append("# No. of blocks = " + nWayDist[1][0].numBlocks()+" #\n\n");
                                pwiseTA.append("# Rearrangement distances based on pairwise LCBs #\n\n");
                                printHeader(pwiseTA,model);
                                printHeader(nwayTA,model);
                        //      PrintStream out = new PrintStream(textArea2OutputStream(nwayOut));
                                nwayTA.append("\n");
                                pwiseTA.append("\n");
                                PrintStream out = new PrintStream(textArea2OutputStream(nwayTA));
                                out.print("# DCJ distance\n");
                                printDistance(out, nWayDist, dcj);
                                out.print("\n# SCJ distance\n");
                                printDistance(out, nWayDist, scj);
                                out.print("\n# Breakpoint distance\n");
                                printDistance(out, nWayDist, bp);
                                DistanceFunction nblks = new DistanceFunction(){
                                        public int distance(DCJ dcj){ return dcj.numBlocks();}
                                };
                                out = new PrintStream(textArea2OutputStream(pwiseTA));
                                out.print("# Number of Blocks\n");
                                printDistance(out, pWiseDist, nblks);
                                out.print("\n# DCJ distance\n");
                                printDistance(out, pWiseDist, dcj);
                                out.print("\n# SCJ distance\n");
                                printDistance(out, pWiseDist, scj);
                                out.print("\n# Breakpoint distance\n");
                                printDistance(out, pWiseDist, bp);
                        } catch (Exception e){
                                nwayTA.replaceRange(error, 0, temp.length());
                                pwiseTA.replaceRange(error, 0, temp.length());
                                e.printStackTrace();
                        }
                } else {
                        adw = new AnalysisDisplayWindow("DCJ - "+model.getSrc().getName(), fWIDTH, fHEIGHT);
                        nwayTA = adw.addContentPanel("DCJ", NWAY_DESC, true);
                        adw.showWindow();
                        nwayTA.append(temp);
                        try {
                                String[] perms = PermutationExporter.getPermStrings(model,true);
                                DCJ dcjDist = new DCJ(perms[0], perms[1]);
                                nwayTA.replaceRange("", 0, temp.length());
                                StringBuilder sb = new StringBuilder();
                                sb.append("no. of blocks = " + dcjDist.numBlocks()+" #\n\n");
                                sb.append("# DCJ distance\n");
                                sb.append("0\n"+dcjDist.dcjDistance()+"\t0\n\n");
                                sb.append("# SCJ distance\n");
                                sb.append("0\n"+dcjDist.scjDistance()+"\t0\n\n");
                                sb.append("# Breakpoint distance\n");
                                sb.append("0\n"+dcjDist.bpDistance()+"\t0\n\n");
                                nwayTA.setText(sb.toString());
                        } catch (Exception e){
                                nwayTA.replaceRange(error, 0, temp.length());
                                System.err.println(error);
                                e.printStackTrace();
                                
                        }
                }
                
        }

        
        private static void printNBlks(PrintStream out, DCJ[][] mat){
                for (int i = 0; i < mat.length; i++){
                        for (int j = 0; j < i; j++){
                                out.print(mat[i][j].numBlocks()+"\t");
                        }
                        out.print("0\n");
                }
        }
        
        private static void printDistance(PrintStream out, DCJ[][] mat, DistanceFunction func){
                for (int i = 0; i < mat.length; i++){
                        for (int j = 0; j < i; j++){
                                out.print(func.distance(mat[i][j])+"\t");
                        }
                        out.print("0\n");
                }
        }
        
        private static void printHeader(JTextArea nblksTA2, XmfaViewerModel model){
                Vector<Genome> v = model.getGenomes();
                Genome[] genomes = v.toArray(new Genome[v.size()]);
                for (int i = 0; i < genomes.length; i++){
                        nblksTA2.append("# "+(i+1)+": " + genomes[i].getDisplayName()+"\n");
                }
        }
        
        private static void printHeader(StringBuilder sb, XmfaViewerModel model){
                Vector<Genome> v = model.getGenomes();
                Genome[] genomes = v.toArray(new Genome[v.size()]);
                for (int i = 0; i < genomes.length; i++){
                        sb.append("# "+(i+1)+": " + genomes[i].getDisplayName()+"\n");
                }
        }
        
        private void loadMatrices(XmfaViewerModel model, DCJ[][] nway, DCJ[][] pwise){
                Vector<Genome> v = model.getGenomes();
                Genome[] genomes = new Genome[v.size()];
                v.toArray(genomes);
                Genome[] pair = new Genome[2];
                String[] nWayPerms = PermutationExporter.getPermStrings(model, genomes,true);
                String[] pairPerm = null;
                DCJ[][] nWayDist = nway;
                DCJ[][] pWiseDist = pwise;
                for (int i = 0; i < genomes.length; i++){
                        for (int j = 0; j < i; j++){
                                pair[0] = genomes[i];
                                pair[1] = genomes[j];
                                pairPerm = PermutationExporter.getPermStrings(model, pair,true);
                                
                                if (!Permutation.equalContents(pairPerm[0], pairPerm[1])){
                                        System.err.println("Unequal contents between genomes "+
                                                        i + " and " + j+"\n" + pairPerm[0] +"\n"+pairPerm[1]);
                                }               
                                nWayDist[i][j] = new DCJ(nWayPerms[i],nWayPerms[j]);
                                pWiseDist[i][j] = new DCJ(pairPerm[0],pairPerm[1]);
                        }
                }               
        }
        
        // add
        


        OutputStream textArea2OutputStream(final JTextArea t)
            { return new OutputStream()
               { JTextArea ta = t;
                 public void write(int b) //minimum implementation of an OutputStream
                  { byte[] bs = new byte[1]; bs[0] = (byte) b;
                    ta.append(new String(bs));
                  }//write
               };
            }
        
        private interface DistanceFunction {
                public int distance(DCJ dcj);
        }

}

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