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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.util.HashMap;
public class RunCommandLine {
ProAlign pa;
PwAlignment pwa;
PwAlignmentLoop pwal;
AlignmentNode root;
public RunCommandLine(ProAlign pa) throws Exception {
ProAlign.log("RunCommandLine");
this.pa = pa;
SequenceReader sr = new SequenceReader();
if(pa.seqfile != null && new File(pa.seqfile).exists()) {
// ..and it's a valid file,
if(sr.fromFile(pa.seqfile)) {
pa.seqs = sr.getSequences();
CheckSequence cs = new CheckSequence();
if(cs.isDna(pa.seqs)){
pa.sm.jcDnaModel();
ProAlign.isDna = true;
} else {
if(ProAlign.protModel.equals("dayhoff")) {
pa.sm.dayhoffProteinModel();
} else if(ProAlign.protModel.equals("jtt")) {
pa.sm.jttProteinModel();
} else {
pa.sm.wagProteinModel();
}
ProAlign.isDna = false;
}
if(!cs.isFromAlphabet(pa.seqs,pa.sm.equateAlphabet)) {
ProAlign.log.println("Sequence reading error: Illegal characters!");
System.out.println("Sequence reading error: Illegal characters!");
if(ProAlign.exitInError) {
System.exit(0);
} else {
throw new Exception("Sequence reading error: Illegal characters");
}
}
} else {
String msg = sr.getErrors();
ProAlign.log.println(msg);
System.out.println(msg);
if(ProAlign.exitInError) {
System.exit(0);
} else {
throw new Exception("Sequence reading error");
}
}
} else {
ProAlign.log.println("Sequence file doesn't exist!");
System.out.println("Sequence file doesn't exist!");
if(ProAlign.exitInError) {
System.exit(0);
} else {
throw new Exception("Sequence file doesn't exist");
}
}
String tree = new String();
TreeReader tr = new TreeReader();
// do a new tree
PwSubstitutionMatrix psm = new PwSubstitutionMatrix();
String pwAlphabet;
int[][] pwSubst;
int gOpen, gExt;
if(ProAlign.isDna){
pwAlphabet = psm.dnaAlphabet;
pwSubst = psm.swdna;
gOpen = -1*pa.pwDnaOpen;
gExt = -1*pa.pwDnaExt;
} else {
pwAlphabet = psm.protAlphabet;
if(pa.pwProtMatrix.equals("pam60")) {
pwSubst = psm.pam60;
} else if(pa.pwProtMatrix.equals("pam160")) {
pwSubst = psm.pam160;
} else if(pa.pwProtMatrix.equals("pam250")) {
pwSubst = psm.pam250;
} else {
pwSubst = psm.pam120;
}
gOpen = -1*pa.pwProtOpen;
gExt = -1*pa.pwProtExt;
}
pwa = new PwAlignment(pwSubst,gOpen,gExt,pwAlphabet,ProAlign.isDna);
if(pa.doTree) {
pwal = new PwAlignmentLoop(pwa,pa.seqs);
tree = pwal.getTree();
if(pa.treefile!=null) {
try {
OutFile newtree = new OutFile(pa.treefile);
newtree.println(tree);
newtree.close();
} catch(Exception e) { }
}
// open an existing tree file
} else if(pa.treefile != null && new File(pa.treefile).exists()) {
String[] treeNodes = tr.getAllNodes(pa.treefile);
CheckTreeAndData chk = new CheckTreeAndData(treeNodes,pa.seqs);
// ..and it's a valid file, set the tree.
if(chk.nodesAreSame()) {
tree = tr.readFile(pa.treefile);
if(tr.isUnRooted) {
TreeNode tn = new TreeNode(tree);
tree = tn.findMiddlePoint();
}
} else {
ProAlign.log.println("Sequence and tree files don't match!");
System.out.println("Sequence and tree files don't match!");
if(ProAlign.exitInError) {
System.exit(0);
} else {
throw new Exception("Sequence and tree files don't match");
}
}
} else {
ProAlign.log.println("Tree file doesn't exist!");
System.out.println("Tree file doesn't exist!");
if(ProAlign.exitInError) {
System.exit(0);
}else {
throw new Exception("Tree file doesn't exist");
}
}
if(tree != null) {
root = new AlignmentNode(pa,tree,0f);
//
if(ProAlign.estimateParameters) {
ParameterEstimates pe = new ParameterEstimates(RunCommandLine.this);
}
//
try {
root.align();
} catch(TraceBackException tbe) {
String msg = tbe.getMessage();
ProAlign.log.println(msg);
System.out.println(msg);
if(ProAlign.exitInError) {
System.exit(0);
}else {
throw new Exception(msg);
}
} catch(Exception e) {
// System.out.println("RunCommandLine: throws an exception");
throw e;
}
// seems to be fine - save results.
if(pa.outformat==1) {
SaveData sd = new SaveData(pa.outfile,1,root);
} else if(pa.outformat==2){
SaveData sd = new SaveData(pa.outfile,2,root);
} else if(pa.outformat==3){
SaveData sd = new SaveData(pa.outfile,3,root);
} else if(pa.outformat==4){
SaveData sd = new SaveData(pa.outfile,4,root);
}
} else {
ProAlign.log.println("Problems with tree!");
System.out.println("Problems with tree!");
if(ProAlign.exitInError) {
System.exit(0);
} else {
throw new Exception("Problems with tree");
}
}
}
}
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