From b606686e01ec42a13f9a91103c7e338925497101 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 1 Jul 2011 23:06:56 +0000
Subject: [PATCH] =?utf8?q?Added=20method=20getCurrentPhylogeny(=20final=20St?=
 =?utf8?q?ring=20format=20)=20written=20by=20Herv=C3=A9=20M=C3=A9nager=20Thi?=
 =?utf8?q?s=20is=20used=20for=20interaction=20with=20JavaScript?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 forester/java/src/org/forester/application/pfam_go.java        |    7 ++++---
 .../src/org/forester/application/simple_node_processor.java    |    4 ++--
 .../java/src/org/forester/archaeopteryx/ArchaeopteryxE.java    |    8 +++-----
 forester/java/src/org/forester/util/ForesterConstants.java     |    7 ++++---
 4 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/forester/java/src/org/forester/application/pfam_go.java b/forester/java/src/org/forester/application/pfam_go.java
index 07e22bb..75f0381 100644
--- a/forester/java/src/org/forester/application/pfam_go.java
+++ b/forester/java/src/org/forester/application/pfam_go.java
@@ -49,8 +49,9 @@ public class pfam_go {
     final static private String E_MAIL                  = "czmasek@burnham.org";
     final static private String WWW                     = "www.phylosoft.org";
 
-    private static void process( final File pfams_file, final List<PfamToGoMapping> mappings, boolean allow_duplicates )
-            throws IOException {
+    private static void process( final File pfams_file,
+                                 final List<PfamToGoMapping> mappings,
+                                 final boolean allow_duplicates ) throws IOException {
         final BufferedReader reader = ForesterUtil.obtainReader( pfams_file );
         String line = "";
         int found_count = 0;
@@ -113,7 +114,7 @@ public class pfam_go {
         }
         final List<String> allowed_options = new ArrayList<String>();
         allowed_options.add( ALLOW_DUPLICATES_OPTION );
-        if ( cla.getNumberOfNames() != 2 && cla.getNumberOfNames() != 3 ) {
+        if ( ( cla.getNumberOfNames() != 2 ) && ( cla.getNumberOfNames() != 3 ) ) {
             printHelp();
             System.exit( -1 );
         }
diff --git a/forester/java/src/org/forester/application/simple_node_processor.java b/forester/java/src/org/forester/application/simple_node_processor.java
index ac60660..033bd9f 100644
--- a/forester/java/src/org/forester/application/simple_node_processor.java
+++ b/forester/java/src/org/forester/application/simple_node_processor.java
@@ -83,8 +83,8 @@ public class simple_node_processor {
     //    }
     private static void processNode( final PhylogenyNode node, final int i ) {
         if ( node.isExternal() ) {
-            String c = "" + node.getNodeData().getBinaryCharacters().getPresentCount();
-            String s = node.getNodeData().getTaxonomy().getScientificName();
+            final String c = "" + node.getNodeData().getBinaryCharacters().getPresentCount();
+            final String s = node.getNodeData().getTaxonomy().getScientificName();
             System.out.println( s + "\t" + c );
         }
     }
diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index de79c15..51f09b0 100644
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -30,9 +30,8 @@ import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
 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;
-
+import org.forester.util.ForesterUtil;
 
 // Use like this:
 // <applet archive="forester.jar"
@@ -313,7 +312,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
      * 
      * @param format must be NH, NHX, NEXUS or PHYLOXML
      * @return the phylogeny string
-     * @author Hervé Ménager
+     * @author Herve Menager
      */
     public String getCurrentPhylogeny( final String format ) {
         removeTextFrame();
@@ -329,14 +328,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             case NEXUS:
                 return getMainPanel().getCurrentPhylogeny().toNexus();
             case PHYLOXML:
-                return getMainPanel().getCurrentPhylogeny().toPhyloXML(-1);
+                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 e7c05f2..9899fd7 100644
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -36,7 +36,8 @@ 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}
-}
-
 
+    public enum PhylogeneticTreeFormats {
+        NH, NHX, NEXUS, PHYLOXML
+    }
+}
-- 
1.7.10.2