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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 native ClustalW.
*/
public class RunClustalw extends Thread {
String tempFolder;
String clustalwPath;
String cmdParameter;
ResultWindow rw;
Process process;
DataInputStream clustalwOut;
/**
* Argument list describing the ClustalW loop.
*/
RunClustalw(ResultWindow rw) {
this.rw = rw;
ProAlign.log("RunClustalw");
clustalwPath = ProAlign.clustalwPath;
tempFolder = ProAlign.tempFolder+File.separator;
if(System.getProperty("os.name").startsWith("Windows")){
File oldFile = new File(tempFolder+"PROALIGN.TRE");
if(oldFile.exists()) {
try {
oldFile.delete();
} catch (Exception ie) {
ProAlign.log.println(" can not delete old guide tree-file!");
}
}
} else {
File oldFile = new File(tempFolder+"proalign.tre");
if(oldFile.exists()) {
try {
oldFile.delete();
} catch (Exception ie) {
ProAlign.log.println(" can not delete old guide tree-file!");
}
}
}
if(System.getProperty("os.name").startsWith("Windows")){
cmdParameter = "clustalw /tree /newtree="+tempFolder+"PROALIGN.TRE /infile="+
tempFolder+"proalign.seq";
} else {
cmdParameter = " -tree -newtree="+tempFolder+"proalign.tre -infile="+
tempFolder+"proalign.seq";
}
start();
}
public void run(){
/**
* Clustalw - make guide tree only!
*/
if(System.getProperty("os.name").startsWith("Windows")) {
int narg = numArg(cmdParameter,"/");
try {
WinClustalw wc = new WinClustalw(narg,cmdParameter);
while(wc.running) {
try{
Thread.currentThread().sleep(500);
} catch(InterruptedException e) {}
}
} catch(Exception ex) {
ProAlign.log("WinClustalw error");
}
} else {
try {
process = Runtime.getRuntime().exec(clustalwPath+cmdParameter);
clustalwOut =
new DataInputStream(new BufferedInputStream(process.getInputStream()));
String str;
while((str = clustalwOut.readLine()) != null) {
if (str.length() > 0) {
ProAlign.log(str);
}
}
} catch(IOException e) { }
}
if(ProAlign.DEBUG) {
ProAlign.log.flush();
}
String filepath;
if(System.getProperty("os.name").startsWith("Windows")){
filepath = ProAlign.tempFolder+File.separator+"PROALIGN.TRE";
} else {
filepath = ProAlign.tempFolder+File.separator+"proalign.tre";
}
File newFile = new File(filepath);
if(!newFile.exists()) { // for some reason ClustalW failed.
String text = "\n ClustalW output not found!\n";
OpenDialog od = new OpenDialog(rw);
od.showDialog("Error!", text);
rw.setRawData(rw.seqs);
rw.setScrollPanes();
} else { // guide tree is fine.
TreeReader tr = new TreeReader();
String[] treeNodes = tr.getAllNodes(filepath);
CheckTreeAndData chk = new CheckTreeAndData(treeNodes, rw.seqs);
if(chk.nodesAreSame()) {
String tree = tr.readFile(filepath);
TreeNode tn = new TreeNode(tree);
tree = tn.findMiddlePoint();
rw.setRawDataAndTree(tree);
rw.setScrollPanes();
} else {
String text = new String("\n Guide tree and sequence \n"+
" file do not match!\n");
OpenDialog od = new OpenDialog(rw);
od.showDialog("Warning!", text);
ProAlign.log.println("ClustalW: nodes and names do not match!");
}
}
}
public int numArg(String cmnd,String csep) {
int narg = 0;
for(int i = 0, j = 0; i < cmnd.length();) {
j = cmnd.indexOf(csep, i);
if (j >= i){
narg++;
i = j;
}
i++;
}
return narg;
}
}
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