Add advanced settings to options files. Fixes #13, #11

molbiodiv · Mar 17, 2016 · 9e90df1 · 9e90df1
1 parent 20abf6a
commit 9e90df1
Showing 1 changed file with 12 additions and 1 deletion.
diff --git a/bcgTreeGUI/src/bcgTree/gui/BcgTree.java b/bcgTreeGUI/src/bcgTree/gui/BcgTree.java
@@ -239,7 +239,18 @@ public void actionPerformed(ActionEvent e) {
  PrintWriter writer;
  try {
  writer = new PrintWriter(outdir+"/options.txt", "UTF-8");
- writer.println("--outdir \""+outdir+"\"");
+ writer.println("--outdir=\""+outdir+"\"");
+ writer.println("--bootstraps="+bootstrapSpinner.getValue());
+ writer.println("--threads="+threadsSpinner.getValue());
+ writer.println("--hmmfile=\""+hmmfileTextField.getText()+"\"");
+ String pSeed = randomSeedPTextField.getText();
+ if(! pSeed.equals("")){
+ writer.println("--raxml-p-parsimonyRandomSeed="+pSeed);
+ }
+ String xSeed = randomSeedXTextField.getText();
+ if(! xSeed.equals("")){
+ writer.println("--raxml-x-rapidBootstrapRandomNumberSeed="+xSeed);
+ }
  for(String p : programPaths.keySet()){
  String path = programPaths.get(p).getText();
  if(!path.equals("")){