X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FNodePanel.java;h=686b348e435a9d69fa2f4c0e556a6997e41ecf26;hb=713d694ab9ab4e0701fd756af1ea2a892f96ade9;hp=768a397bf28452180d5471591b5d0d5756898d44;hpb=b94510dea3a694b982079cae77805f1a47986b9b;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/NodePanel.java b/forester/java/src/org/forester/archaeopteryx/NodePanel.java
index 768a397..686b348 100644
--- a/forester/java/src/org/forester/archaeopteryx/NodePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/NodePanel.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -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;
@@ -231,16 +232,13 @@ class NodePanel extends JPanel implements TreeSelectionListener {
         }
     }
 
-   
-    
-    
     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() ) );
@@ -264,12 +262,11 @@ class NodePanel extends JPanel implements TreeSelectionListener {
                 if ( no_tax > 0 ) {
                     addSubelement( category, "External nodes without taxonomy", String.valueOf( no_tax ) );
                 }
-              
             }
         }
         if ( !phylogeny_node.isRoot() ) {
-            addSubelement( category, "Depth", String.valueOf( PhylogenyMethods.calculateDepth( phylogeny_node ) ) );
-            final double d = PhylogenyMethods.calculateDistanceToRoot( phylogeny_node );
+            addSubelement( category, "Depth", String.valueOf( phylogeny_node.calculateDepth() ) );
+            final double d = phylogeny_node.calculateDistanceToRoot();
             if ( d > 0 ) {
                 addSubelement( category, "Distance to root", String.valueOf( ForesterUtil.FORMATTER_6.format( d ) ) );
             }
@@ -320,7 +317,7 @@ class NodePanel extends JPanel implements TreeSelectionListener {
         addSubelement( category, DIST_DESCRIPTION, dist.getDesc() );
         if ( ( dist.getPoints() != null ) && ( dist.getPoints().size() > 0 ) ) {
             final Point p0 = dist.getPoints().get( 0 );
-            if ( p0 != null ) {
+            if ( ( p0 != null ) && !Point.isSeemsEmpty( p0 ) ) {
                 addSubelement( category, DIST_GEODETIC_DATUM, p0.getGeodeticDatum() );
                 addSubelement( category, DIST_LATITUDE, String.valueOf( p0.getLatitude() ) );
                 addSubelement( category, DIST_LONGITUDE, String.valueOf( p0.getLongitude() ) );