Merge branch 'develop' - version 1.0.10

molbiodiv · Mar 7, 2017 · 438effb · 438effb
2 parents c71db8e + a396b5a
commit 438effb
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Showing 5 changed files with 36 additions and 6 deletions.
diff --git a/README.org b/README.org
@@ -161,6 +161,11 @@ Options:
         file to find out the actual value). Note: you can abbreviate options
         (as long as they stay unique) so --raxml-p=12345 is equivalent to
         --raxml-p-parsimonyRandomSeed=12345
+
+    [--raxml-args "<ARGS>"]
+        Arbitrary options to pass through to RAxML. The ARGS part should be
+        in quotes and is appended to the RAxML command as given.
+
 #+END_SRC
 ** Results
 The results all end up in the directory specified via --outdir (or bcgTree if none is specified).
@@ -202,6 +207,9 @@ The font is from [[fontlibrary.org]]:
  - [[https://fontlibrary.org/en/font/ranchers][Ranchers]] ([[http://scripts.sil.org/cms/scripts/page.php?site_id=nrsi&id=OFL][SIL Open Font License]])
 ** Changes
 [[https://travis-ci.org/molbiodiv/bcgTree][https://travis-ci.org/molbiodiv/bcgTree.svg?branch=master]]
+*** v1.0.10 <2017-03-07 Di>
+ - Fix GUI, add scrollbar (#23)
+ - Add parameter --raxml-args (#22)
 *** v1.0.9 <2017-03-03 Fr>
  - Add parameters --min-proteomes and --all-proteomes (#21)
 *** v1.0.8 <2016-09-07 Mi>

diff --git a/bcgTreeGUI/bcgTree.jar b/bcgTreeGUI/bcgTree.jar
diff --git a/bcgTreeGUI/src/bcgTree/gui/BcgTree.java b/bcgTreeGUI/src/bcgTree/gui/BcgTree.java
@@ -36,6 +36,7 @@
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JProgressBar;
+import javax.swing.JScrollPane;
 import javax.swing.JSpinner;
 import javax.swing.JTextField;
 import javax.swing.SpinnerNumberModel;
@@ -45,7 +46,7 @@
 
 public class BcgTree extends JFrame {
 	private static final long serialVersionUID = 1L;
-	public static final String VERSION = "1.0.9";
+	public static final String VERSION = "1.0.10";
 	private static final int DEFAULT_TEXTFIELD_COLUMNS = 30;
 
 	public static void main(String[] args) {
@@ -77,6 +78,7 @@ public static void main(String[] args) {
 	private JTextField hmmfileTextField;
 	private JSpinner minProteomesSpinner;
 	private JCheckBox allProteomesCheckbox;
+	private JTextField raxmlArgsTextField;
 
 	public BcgTree(){
 		self = this;
@@ -107,8 +109,9 @@ public void initGUI(){
 		mainPanel.setLayout(new GridLayout(1, 2));
 		this.add(mainPanel, BorderLayout.CENTER);
 		settingsPanel = new JPanel();
+		JScrollPane settingsScrollPane = new JScrollPane(settingsPanel);
 		settingsPanel.setLayout(new GridBagLayout());
-		mainPanel.add(settingsPanel);
+		mainPanel.add(settingsScrollPane);
 		JPanel logPanel = new JPanel();
 		logPanel.setLayout(new BorderLayout());
 		mainPanel.add(logPanel);
@@ -211,7 +214,7 @@ public void actionPerformed(ActionEvent e) {
 	}
 
 	private JPanel getAdvancedSettingsPanel(){
-		JPanel advancedSettingsPanel = new JPanel(new GridLayout(7, 2));
+		JPanel advancedSettingsPanel = new JPanel(new GridLayout(8, 2));
 		advancedSettingsPanel.add(new JLabel("--bootstraps"));
 		bootstrapSpinner = new JSpinner(new SpinnerNumberModel(10, 1, 1000, 1));
 		advancedSettingsPanel.add(bootstrapSpinner);
@@ -224,6 +227,9 @@ private JPanel getAdvancedSettingsPanel(){
 		advancedSettingsPanel.add(new JLabel("--raxml-p-parsimonyRandomSeed"));
 		randomSeedPTextField = new JTextField("", DEFAULT_TEXTFIELD_COLUMNS);
 		advancedSettingsPanel.add(randomSeedPTextField);
+		advancedSettingsPanel.add(new JLabel("--raxml-args"));
+		raxmlArgsTextField = new JTextField("", DEFAULT_TEXTFIELD_COLUMNS);
+		advancedSettingsPanel.add(raxmlArgsTextField);
 		advancedSettingsPanel.add(new JLabel("--hmmfile"));
 		hmmfileTextField = new JTextField(System.getProperty("user.dir")+"/../data/essential.hmm", DEFAULT_TEXTFIELD_COLUMNS);
 		advancedSettingsPanel.add(hmmfileTextField);
@@ -283,6 +289,10 @@ public void actionPerformed(ActionEvent e) {
 				if(! xSeed.equals("")){
 					writer.println("--raxml-x-rapidBootstrapRandomNumberSeed="+xSeed);
 				}
+				String raxmlArgs = raxmlArgsTextField.getText();
+				if(! raxmlArgs.equals("")){
+					writer.println("--raxml-args=\""+raxmlArgs+"\"");
+				}
 				for(String p : programPaths.keySet()){
 					String path = programPaths.get(p).getText();
 					if(!path.equals("")){						

diff --git a/bin/bcgTree.pl b/bin/bcgTree.pl
@@ -198,6 +198,17 @@ =head1 OPTIONS
 
 =back
 
+=item [--raxml-args "<ARGS>"]
+
+Arbitrary options to pass through to RAxML.
+The ARGS part should be in quotes and is appended to the RAxML command as given.
+
+=cut
+
+$options{'raxml-args=s'} = \( my $opt_raxml_args = "");
+
+=back
+
 =head1 CODE
 
 =cut
@@ -242,7 +253,8 @@ =head1 CODE
 	'hmmfile' => $opt_hmmfile,
 	'raxml-p' => $opt_raxml_p,
 	'raxml-x' => $opt_raxml_x,
-    'min-proteomes' => $opt_min_proteomes
+    'min-proteomes' => $opt_min_proteomes,
+    'raxml-args' => $opt_raxml_args
 });
 $bcgTree->check_existence_of_fasta_files();
 $bcgTree->rename_fasta_headers();

diff --git a/lib/bcgTree.pm b/lib/bcgTree.pm
@@ -11,7 +11,7 @@ use File::Path qw(make_path);
 use File::Spec;
 use Fasta::Parser;
 
-our $VERSION = '1.0.9';
+our $VERSION = '1.0.10';
 
 my $L = Log::Log4perl::get_logger();
 
@@ -276,7 +276,7 @@ sub run_raxml{
 	my $self = shift;
 	my $out = $self->{'outdir'};
 	my $msg = "raxml on $out/full_alignment.concat.fa";
-	my $cmd = $self->{'raxml-bin'}." -f a -m GTRGAMMA -p ".$self->{'raxml-p'}." -q $out/full_alignment.concat.partition -s $out/full_alignment.concat.fa -w ".File::Spec->rel2abs( $out )." -n final -T ".$self->{'threads'}." -x ".$self->{'raxml-x'}." -N ".$self->{'bootstraps'};
+	my $cmd = $self->{'raxml-bin'}." -f a -m GTRGAMMA -p ".$self->{'raxml-p'}." -q $out/full_alignment.concat.partition -s $out/full_alignment.concat.fa -w ".File::Spec->rel2abs( $out )." -n final -T ".$self->{'threads'}." -x ".$self->{'raxml-x'}." -N ".$self->{'bootstraps'}." ".$self->{'raxml-args'};
 	$self->run_command($cmd, $msg);
 	$L->info("Finished bcgTree.");
 }