From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 1 Jul 2011 23:03:39 +0000 (+0000)
Subject: Added method getCurrentPhylogeny( final String format ) written by Hervé Ménager
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=09d0269700d3108a10d8e349e37384a9cad551ea;p=jalview.git

Added method getCurrentPhylogeny( final String format ) written by Hervé Ménager
This is used for interaction with JavaScript
---

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 7dbed25..de79c15 100644
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -31,6 +31,8 @@ import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.data.SequenceRelation;
 import org.forester.util.ForesterUtil;
+import org.forester.util.ForesterConstants;
+
 
 // Use like this:
 // <applet archive="forester.jar"
@@ -306,6 +308,35 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         repaint();
     }
 
+    /**
+     * This method returns the current phylogeny as a string in the chosen format
+     * 
+     * @param format must be NH, NHX, NEXUS or PHYLOXML
+     * @return the phylogeny string
+     * @author Hervé Ménager
+     */
+    public String getCurrentPhylogeny( final String format ) {
+        removeTextFrame();
+        if ( ( getMainPanel().getCurrentPhylogeny() == null ) || getMainPanel().getCurrentPhylogeny().isEmpty()
+                || ( getMainPanel().getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
+            return new String();
+        }
+        switch ( ForesterConstants.PhylogeneticTreeFormats.valueOf( format ) ) {
+            case NH:
+                return getMainPanel().getCurrentPhylogeny().toNewHampshire();
+            case NHX:
+                return getMainPanel().getCurrentPhylogeny().toNewHampshireX();
+            case NEXUS:
+                return getMainPanel().getCurrentPhylogeny().toNexus();
+            case PHYLOXML:
+                return getMainPanel().getCurrentPhylogeny().toPhyloXML(-1);
+            default:
+                break;
+        }
+        return new String();
+    }
+
+
     void buildFontSizeMenu() {
         _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
         _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index 7fd5c84..e7c05f2 100644
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -36,4 +36,7 @@ public final class ForesterConstants {
     public final static String  UTF8                        = "UTF-8";
     public final static String  PHYLO_XML_REFERENCE         = "Han MV and Zmasek CM (2009): \"phyloXML: XML for evolutionary biology and comparative genomics\", BMC Bioinformatics 10:356";
     public final static boolean RELEASE                     = false;
+    public enum PhylogeneticTreeFormats {NH, NHX, NEXUS, PHYLOXML}
 }
+
+