X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FNodePanel.java;h=c7a9ce815d3f0bcbe7f9d91519af5f09b8bf2618;hb=7ad84913635263ddc191fcbebd8a9bd46a9ac7e3;hp=ebed53080cc5a491573e7221f623dec60d9a8bfc;hpb=c94d818879d93f5a794f905a6312982d348b2752;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/NodePanel.java b/forester/java/src/org/forester/archaeopteryx/NodePanel.java
index ebed530..c7a9ce8 100644
--- a/forester/java/src/org/forester/archaeopteryx/NodePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/NodePanel.java
@@ -50,6 +50,7 @@ import org.forester.phylogeny.data.Date;
 import org.forester.phylogeny.data.Distribution;
 import org.forester.phylogeny.data.Event;
 import org.forester.phylogeny.data.PhylogenyData;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.data.Point;
 import org.forester.phylogeny.data.PropertiesMap;
 import org.forester.phylogeny.data.Property;
@@ -210,13 +211,34 @@ class NodePanel extends JPanel implements TreeSelectionListener {
         }
     }
 
+    private static void addLineage( final DefaultMutableTreeNode top,
+                                    final List<String> lineage,
+                                    final DefaultMutableTreeNode category ) {
+        if ( ( lineage != null ) && ( lineage.size() > 0 ) ) {
+            final StringBuilder sb = new StringBuilder();
+            for( final String lin : lineage ) {
+                if ( !ForesterUtil.isEmpty( lin ) ) {
+                    sb.append( lin );
+                    sb.append( " > " );
+                }
+            }
+            String str = null;
+            if ( sb.length() > 1 ) {
+                str = sb.substring( 0, sb.length() - 3 );
+            }
+            if ( !ForesterUtil.isEmpty( str ) ) {
+                addSubelement( category, "Lineage", str );
+            }
+        }
+    }
+
     private static void addBasics( final DefaultMutableTreeNode top,
                                    final PhylogenyNode phylogeny_node,
                                    final String name ) {
         final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
         top.add( category );
         addSubelement( category, NODE_NAME, phylogeny_node.getName() );
-        if ( phylogeny_node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
+        if ( phylogeny_node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
             addSubelement( category,
                            NODE_BRANCH_LENGTH,
                            ForesterUtil.FORMATTER_6.format( phylogeny_node.getDistanceToParent() ) );
@@ -226,18 +248,6 @@ class NodePanel extends JPanel implements TreeSelectionListener {
                 addSubelement( category, CONFIDENCE, conf.asText().toString() );
             }
         }
-        if ( ( phylogeny_node.getBranchData().getBranchWidth() != null )
-                && ( phylogeny_node.getBranchData().getBranchWidth().getValue() != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) ) {
-            addSubelement( category,
-                           NODE_BRANCH_WIDTH,
-                           ForesterUtil.FORMATTER_3.format( phylogeny_node.getBranchData().getBranchWidth().getValue() ) );
-        }
-        if ( ( phylogeny_node.getBranchData().getBranchColor() != null ) ) {
-            Color c = phylogeny_node.getBranchData().getBranchColor().getValue();
-            addSubelement( category,
-                           NODE_BRANCH_COLOR,
-                            c.getRed() + ", " + c.getGreen() + ", "+ c.getBlue() );
-        }
         if ( !phylogeny_node.isExternal() ) {
             addSubelement( category, "Children", String.valueOf( phylogeny_node.getNumberOfDescendants() ) );
             addSubelement( category,
@@ -252,10 +262,6 @@ class NodePanel extends JPanel implements TreeSelectionListener {
                 if ( no_tax > 0 ) {
                     addSubelement( category, "External nodes without taxonomy", String.valueOf( no_tax ) );
                 }
-                //TODO remove me...
-                for( final Taxonomy taxonomy : distinct_tax.keySet() ) {
-                    System.out.println( taxonomy + ": " + distinct_tax.get( taxonomy ) );
-                }
             }
         }
         if ( !phylogeny_node.isRoot() ) {
@@ -265,6 +271,16 @@ class NodePanel extends JPanel implements TreeSelectionListener {
                 addSubelement( category, "Distance to root", String.valueOf( ForesterUtil.FORMATTER_6.format( d ) ) );
             }
         }
+        if ( ( phylogeny_node.getBranchData().getBranchWidth() != null )
+                && ( phylogeny_node.getBranchData().getBranchWidth().getValue() != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) ) {
+            addSubelement( category,
+                           NODE_BRANCH_WIDTH,
+                           ForesterUtil.FORMATTER_3.format( phylogeny_node.getBranchData().getBranchWidth().getValue() ) );
+        }
+        if ( ( phylogeny_node.getBranchData().getBranchColor() != null ) ) {
+            final Color c = phylogeny_node.getBranchData().getBranchColor().getValue();
+            addSubelement( category, NODE_BRANCH_COLOR, c.getRed() + ", " + c.getGreen() + ", " + c.getBlue() );
+        }
     }
 
     private static void addBinaryCharacters( final DefaultMutableTreeNode top,
@@ -341,7 +357,7 @@ class NodePanel extends JPanel implements TreeSelectionListener {
         top.add( category );
         for( final String key : properties_map.keySet() ) {
             final Property prop = properties_map.get( key );
-            category.add( new DefaultMutableTreeNode( prop.getRef() + " " + prop.getValue() + " " + prop.getUnit()
+            category.add( new DefaultMutableTreeNode( prop.getRef() + "=" + prop.getValue() + " " + prop.getUnit()
                     + " [" + prop.getAppliesTo().toString() + "]" ) );
         }
     }
@@ -393,6 +409,9 @@ class NodePanel extends JPanel implements TreeSelectionListener {
         if ( ( tax.getUris() != null ) && !tax.getUris().isEmpty() ) {
             addUris( top, tax.getUris(), category );
         }
+        if ( ( tax.getLineage() != null ) && !tax.getLineage().isEmpty() ) {
+            addLineage( top, tax.getLineage(), category );
+        }
     }
 
     private static void createNodes( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node ) {