X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FNodePanel.java;h=4cfb7b2cb6d027a3f81e3ee7b82f9ca45aa9bb9a;hb=045ed0731ed1997f6ccf41b2a7688d028ea73a0a;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..4cfb7b2 100644
--- a/forester/java/src/org/forester/archaeopteryx/NodePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/NodePanel.java
@@ -210,6 +210,27 @@ 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 ) {
@@ -226,18 +247,6 @@ 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 +261,10 @@ 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 ) );
-                }
+                //TODO remove me... maybe make me into a method?
+                //for( final Taxonomy taxonomy : distinct_tax.keySet() ) {
+                //    System.out.println( taxonomy + ": " + distinct_tax.get( taxonomy ) );
+                //}
             }
         }
         if ( !phylogeny_node.isRoot() ) {
@@ -265,6 +274,16 @@ 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,
@@ -393,6 +412,9 @@ 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 ) {