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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;
public class ReadArguments {
ReadArguments(ProAlign pa, String[] args) {
ProAlign.log("ReadArguments");
for(int i=0; i<args.length; i++) {
// sequence file
if(args[i].startsWith("-seqfile=")) {
pa.seqfile = args[i].substring(args[i].indexOf("=")+1);
ProAlign.log.println(" sequence file: "+pa.seqfile);
// guide tree file
} else if(args[i].startsWith("-treefile=")) {
pa.treefile = args[i].substring(args[i].indexOf("=")+1);
ProAlign.log.println(" tree file: "+pa.treefile);
// no GUI
} else if(args[i].startsWith("-nogui")) {
pa.nogui = true;
ProAlign.log.println(" no GUI: true");
// do tree
} else if(args[i].startsWith("-newtree")) {
pa.doTree = true;
ProAlign.log.println(" do tree: true");
// sample from post. probabilities
} else if(args[i].startsWith("-sample")) {
pa.trackBest = false;
ProAlign.log.println(" sample backtrace path: true");
// gap frequency
} else if(args[i].startsWith("-gapfreq=")) {
if(args[i].endsWith("=estimate")) {
pa.estimateGapFreq = true;
pa.estimateParameters = true ;
ProAlign.log.println(" gap frequency: estimate");
} else {
double tmp = new Double(
args[i].substring(args[i].indexOf("=")+1)).doubleValue();
if(tmp>0d && tmp<0.5d) {
pa.gapFreq = tmp;
ProAlign.log.println(" gap frequency: "+tmp);
} else {
ProAlign.log.println(" bad value: gap frequency "+tmp);
}
}
// gap probability
} else if(args[i].startsWith("-gapprob=")) {
if(args[i].endsWith("=estimate")) {
pa.estimateGapProb = true;
pa.estimateParameters = true ;
ProAlign.log.println(" gap probability: estimate");
} else {
double tmp = new Double(
args[i].substring(args[i].indexOf("=")+1)).doubleValue();
if(tmp>0d && tmp<0.5d) {
pa.gapProb = tmp;
ProAlign.log.println(" gap probability: "+tmp);
} else {
ProAlign.log.println(" bad value: gap probability "+tmp);
}
}
// delta for HMM model
} else if(args[i].startsWith("-delta=")) {
if(args[i].endsWith("=estimate")) {
pa.estimateDelta = true;
pa.estimateParameters = true ;
ProAlign.log.println(" HMM delta: estimate");
} else {
double tmp = new Double(
args[i].substring(args[i].indexOf("=")+1)).doubleValue();
if(tmp>0d && tmp<0.5d) {
pa.modelDelta = tmp;
ProAlign.log.println(" HMM delta: "+tmp);
} else {
ProAlign.log.println(" bad value: HMM delta "+tmp);
}
}
// epsilon for HMM model
} else if(args[i].startsWith("-epsilon=")) {
if(args[i].endsWith("=estimate")) {
pa.estimateEpsilon = true;
pa.estimateParameters = true ;
ProAlign.log.println(" HMM epsilon: estimate");
} else {
double tmp = new Double(
args[i].substring(args[i].indexOf("=")+1)).doubleValue();
if(tmp>0d && tmp<1.0d) {
pa.modelEpsilon = tmp;
ProAlign.log.println(" HMM epsilon: "+tmp);
} else {
ProAlign.log.println(" bad value: HMM epsilon "+tmp);
}
}
// band width
} else if(args[i].startsWith("-bwidth=")) {
int tmp = new Integer(
args[i].substring(args[i].indexOf("=")+1)).intValue();
if(tmp>5) {
pa.bandWidth = tmp;
ProAlign.log.println(" band width: "+tmp);
} else {
ProAlign.log.println(" bad value: band width "+tmp);
}
// distance scale
} else if(args[i].startsWith("-distscale=")) {
double tmp = new Double(
args[i].substring(args[i].indexOf("=")+1)).doubleValue();
if(tmp>0d && tmp<2.0d) {
pa.distScale = tmp;
ProAlign.log.println(" distance scale: "+tmp);
} else {
ProAlign.log.println(" bad value: distance scale "+tmp);
}
// multiple hits
} else if(args[i].startsWith("-nocorrection")) {
pa.correctMultiple = false ;
ProAlign.log.println(" correctMultiple: "+pa.correctMultiple);
// terminal gaps
} else if(args[i].startsWith("-penalize")) {
if(args[i].endsWith("=true")) {
pa.penalizeTerminal = true ;
} else if(args[i].endsWith("=false")) {
pa.penalizeTerminal = false ;
}
ProAlign.log.println(" penalizeTerminal: "+pa.penalizeTerminal);
// mean post prob.
} else if(args[i].startsWith("-writemean")) {
pa.writeMean = true ;
ProAlign.log.println(" output mean: "+pa.writeMean);
// all post prob.
} else if(args[i].startsWith("-writeall")) {
pa.writeAll = true ;
ProAlign.log.println(" output all: "+pa.writeAll);
// root characters
} else if(args[i].startsWith("-writeroot")) {
pa.writeRoot = true ;
ProAlign.log.println(" output root: "+pa.writeRoot);
// protein model
} else if(args[i].startsWith("-wag")) {
ProAlign.protModel = "wag";
ProAlign.isDna = false;
ProAlign.log.println(" protein model: "+ProAlign.protModel);
} else if(args[i].startsWith("-dayhoff")) {
ProAlign.protModel = "dayhoff";
ProAlign.isDna = false;
ProAlign.log.println(" protein model: "+ProAlign.protModel);
} else if(args[i].startsWith("-jtt")) {
ProAlign.protModel = "jtt";
ProAlign.isDna = false;
ProAlign.log.println(" protein model: "+ProAlign.protModel);
// trailing
} else if(args[i].startsWith("-notrailing")) {
pa.removeTrailing = false ;
ProAlign.log.println(" removeTrailing: "+pa.removeTrailing);
// allowed trailing
} else if(args[i].startsWith("-trailing=")) {
int tmp = new Integer(
args[i].substring(args[i].indexOf("=")+1)).intValue();
if(tmp>5 && tmp < pa.bandWidth/2) {
pa.offset = tmp;
ProAlign.log.println(" trailing: "+tmp);
} else {
ProAlign.log.println(" bad value: trailing "+tmp);
}
// output file
} else if(args[i].startsWith("-outfile=")) {
pa.outfile = args[i].substring(args[i].indexOf("=")+1);
ProAlign.log.println(" output file: "+pa.outfile);
// output format
} else if(args[i].startsWith("-outformat=")) {
if(args[i].substring(args[i].indexOf("=")+1).equalsIgnoreCase("fasta")){
pa.outformat = 2;
ProAlign.log.println(" outformat: PIR");
} else if(args[i].substring(args[i].indexOf("=")+1).equalsIgnoreCase("PIR")){
pa.outformat = 2;
ProAlign.log.println(" outformat: PIR");
} else if(args[i].substring(args[i].indexOf("=")+1).equalsIgnoreCase("nexus")){
pa.outformat = 1;
ProAlign.log.println(" outformat: nexus");
} else if(args[i].substring(args[i].indexOf("=")+1).equalsIgnoreCase("phylip")){
pa.outformat = 3;
ProAlign.log.println(" outformat: phylip");
} else if(args[i].substring(args[i].indexOf("=")+1).equalsIgnoreCase("msf")){
pa.outformat = 4;
ProAlign.log.println(" outformat: msf");
}
// stay quiet, no log
} else if(args[i].startsWith("-quiet")) {
pa.DEBUG = false;
ProAlign.log.println(" quiet...");
ProAlign.log.flush();
} else {
ProAlign.log.println("Unrecognized paramter: "+args[i]);
ProAlign.log.flush();
}
}
}
}
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