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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.math.BigDecimal;
import java.io.DataInputStream;
import java.io.BufferedInputStream;
/**
* Running alignment in a separate thread
*/
public class RunMultiple extends Thread {
ResultWindow rw;
RunMultiple(ResultWindow rw) {
this.rw = rw;
ProAlign.log("RunMultiple");
start();
}
public void run() {
boolean isError = false;
String errorMsg = new String();
try {
rw.root.align();
} catch(TraceBackException tbe) {
isError = true;
errorMsg = tbe.getMessage();
} catch(Exception e) { }
if(isError) {
OpenDialog od = new OpenDialog(rw);
od.showDialog("Error!", "\n "+errorMsg+"\n Try to increase the band width.\n");
rw.file[1].setEnabled(true); // open alignment
rw.file[2].setEnabled(false); // save alignment
rw.data[0].setEnabled(true); // import data
rw.data[1].setEnabled(true); // import guide tree
rw.align[0].setEnabled(true); // do guide tree NOT YET
rw.align[1].setEnabled(true); // do multiple
rw.align[2].setEnabled(true); // do complete NOT YET
rw.align[3].setEnabled(true); // sample
rw.align[4].setEnabled(false); // remove gaps
rw.dm.setEnabled(true); // import
rw.em.setEnabled(false); // export
} else {
rw.setAlignedData(rw.root);
rw.setScrollPanes();
if(rw.root.isBandWarning()) {
String text = new String(
"\n Traceback path came very close\n to the band edge."+
" Alignment may\n not be the correct one!");
OpenDialog od = new OpenDialog(rw);
od.showDialog("Warning!",text);
}
if(!rw.root.isUnique()) {
String text = new String(
"\n There exist more than one possible\n alignment. The backtrace "+
"path was\n chosen "+rw.root.getSampleTimes()+" times randomly between\n"+
" two equally good alternatives.\n");
OpenDialog od = new OpenDialog(rw);
od.showDialog("Notice!",text);
}
}
}
}
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