X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=24cb223221b9fcc9df3f1a8e193ff1b6c8aee8eb;hb=aaac4312b5a1356278bad15c79d0e97de8823c72;hp=7825bb7b108134759cec1f780e8981a95df5a989;hpb=e6ea1a1dcb0a9b96cad1bc08c3b80a6f876344d2;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 7825bb7..24cb223 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -2472,7 +2472,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         if ( additional_nodes != null ) {
             for( final PhylogenyNode an : additional_nodes ) {
-               // n.getBranchData().setBranchColor( new BranchColor( c ) );
                 for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) {
                     it.next().getBranchData().setBranchColor( new BranchColor( c ) );
                 }
@@ -2821,7 +2820,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         return getTreeFontSet().getFontMetricsLarge();
     }
 
-    private List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
+    List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
         final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
         if ( getFoundNodes0() != null ) {
             for( final Long id : getFoundNodes0() ) {
@@ -4675,7 +4674,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         float new_x = 0;
         float new_x_min = Float.MAX_VALUE;
-        final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
+        final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 );
         float min_dist = 1.5f;
         if ( !disallow_shortcutting ) {
             //   System.out.println( dynamic_hiding_factor );
@@ -4750,7 +4749,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                                     final PhylogenyNode node,
                                                     final boolean to_graphics_file,
                                                     final boolean to_pdf ) {
-        if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
+        if ( isNodeDataInvisible( node ) && !( to_graphics_file || to_pdf ) ) {
             return;
         }
         if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {