in progress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / TreePanel.java

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 7825bb7..24cb223 100644 (file)
--- 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() ) ) {