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/**
* Title: ProAlign<p>
* Description: <p>
* Copyright: Copyright (c) Ari Loytynoja<p>
* License: GNU GENERAL PUBLIC LICENSE<p>
* @see http://www.gnu.org/copyleft/gpl.html
* Company: ULB<p>
* @author Ari Loytynoja
* @version 1.0
*/
package proalign;
import java.io.File;
import java.io.IOException;
import java.io.InvalidClassException;
import java.io.FileOutputStream;
import java.io.ObjectOutputStream;
class SampleLoop extends Thread {
SampleAlignments sl;
AlignmentNode best;
AlignmentNode current;
double bestEnd = 0d;
int currentRun = 0;
int maxRun;
SampleLoop(SampleAlignments sl) {
this.sl = sl;
current = sl.rw.root;
maxRun = sl.numRun;
ProAlign.log("SampleLoop");
sl.write("\n Sampling "+maxRun+" alignments: ");
if(sl.writeResults) {
String[] names = current.getInternalNames();
String str = "number,length,total";
for(int i=0; i<names.length; i++) {
str += ","+names[i];
}
sl.resultOut.println(str);
sl.resultOut.flush();
}
start();
}
public void run(){
while(sl.isRunning && currentRun < maxRun) {
boolean isError = false;
String errorMsg = new String();
try {
current.align();
} catch(TraceBackException tbe) {
isError = true;
errorMsg = tbe.getMessage();
} catch(Exception e) { }
// Threw an exception during the alignment
if(isError) {
OpenDialog od = new OpenDialog(sl);
od.showDialog("Error!", "\n "+errorMsg+"\n Try to increase the band width.\n");
break;
} else {
if(current.isBandWarning()) {
sl.write("Traceback path came very close\n to the band edge."+
" Alignment may\n not be the correct one!");
}
}
if(currentRun==0) {
bestEnd = current.sumViterbiEnd();
sl.rw.root = current;
sl.rw.setAlignedData(sl.rw.root);
sl.rw.setScrollPanes();
sl.rw.messageText.setText(" Sample "+(currentRun+1)+"/"+maxRun+": "+current.sumViterbiEnd());
} else if (current.sumViterbiEnd() > bestEnd) {
bestEnd = current.sumViterbiEnd();
sl.rw.root = current;
sl.rw.setAlignedData(sl.rw.root);
sl.rw.setScrollPanes();
sl.rw.messageText.setText(" Sample "+(currentRun+1)+"/"+maxRun+": "+current.sumViterbiEnd());
}
if(sl.writeAlignments) {
String path = sl.folderPath+File.separator+(currentRun+1)+"."+ProAlign.fileExt;
try {
ObjectOutputStream os =
new ObjectOutputStream(new FileOutputStream(path));
os.writeObject((AlignmentNode) current);
os.flush();
os.close();
} catch(IOException ioe) {
ProAlign.log.println("Sample exception1: "+path+"\n"+ioe.toString());
ProAlign.log.flush();
//ioe.printStackTrace();
}
catch(Exception oe) {
ProAlign.log.println("Sample exception2: "+path+"\n"+oe.toString());
ProAlign.log.flush();
//oe.printStackTrace();
}
}
if(sl.writeNexus) {
String path = sl.nexusPath+File.separator+(currentRun+1)+".nex";
SaveData sd = new SaveData(path,1,current);
}
if(sl.writeFasta) {
String path = sl.fastaPath+File.separator+(currentRun+1)+".pir";
SaveData sd = new SaveData(path,2,current);
}
sl.write("Sample "+(currentRun+1)+"/"+maxRun+": "+current.sumViterbiEnd()+"; best: "+bestEnd);
if(sl.writeResults) {
double[] vit = current.getInternalViterbiEnd();
String str = (currentRun+1)+","+current.cellPath.length+","+current.sumViterbiEnd();
for(int i=0; i<vit.length; i++) {
str += ","+vit[i];
}
sl.resultOut.println(str);
sl.resultOut.flush();
}
if(ProAlign.DEBUG) {
ProAlign.log.println(" sample number "+currentRun);
ProAlign.log.flush();
}
currentRun++;
}
}
}
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