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[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 c96f82f..0f04f1e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -165,6 +165,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                                                                                         12 );
     private static final float           ROUNDED_D                                          = 8;
     private final static long            serialVersionUID                                   = -978349745916505029L;
+    private static final BasicStroke     STROKE_0025                                        = new BasicStroke( 0.025f );
     private static final BasicStroke     STROKE_005                                         = new BasicStroke( 0.05f );
     private static final BasicStroke     STROKE_01                                          = new BasicStroke( 0.1f );
     private static final BasicStroke     STROKE_025                                         = new BasicStroke( 0.25f );
@@ -1637,23 +1638,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     _nodes_in_preorder[ i++ ] = it.next();
                 }
             }
-            //final PhylogenyNodeIterator it;
-            //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
-            //    paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
-            //            && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
-            //}
-            
-            
-            final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 ) || getControlPanel().isUseVisualStyles()
-                    || getOptions().isShowDefaultNodeShapesForMarkedNodes()
+            final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 )
+                    || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()
                     || ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() )
                     || ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() )
-                    || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() );
-          
-            
+                    || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() )
+                    || to_graphics_file || to_pdf;
             for( final PhylogenyNode element : _nodes_in_preorder ) {
-                paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()
-                        && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
+                paintNodeRectangular( g,
+                                      element,
+                                      to_pdf,
+                                      getControlPanel().isDynamicallyHideData() && ( dynamic_hiding_factor > 1 ),
+                                      dynamic_hiding_factor,
+                                      to_graphics_file,
+                                      disallow_shortcutting );
             }
             if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
                 if ( !( to_graphics_file || to_pdf ) ) {
@@ -4714,7 +4712,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                              final boolean to_pdf,
                                              final boolean dynamically_hide,
                                              final int dynamic_hiding_factor,
-                                             final boolean to_graphics_file ) {
+                                             final boolean to_graphics_file,
+                                             final boolean disallow_shortcutting ) {
         final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
         if ( node.isCollapse() ) {
             if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
@@ -4740,11 +4739,6 @@ 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 ) || getControlPanel().isUseVisualStyles()
-                || getOptions().isShowDefaultNodeShapesForMarkedNodes()
-                || ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() )
-                || ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() )
-                || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() );
         float min_dist = 1.5f;
         if ( !disallow_shortcutting ) {
             if ( dynamic_hiding_factor > 4000 ) {
@@ -4786,7 +4780,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 final float diff_y = node.getYcoord() - y2;
                 final float diff_x = node.getXcoord() - new_x;
                 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
-                        || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
+                        || ( diff_x < -min_dist ) ) {
                     paintBranchRectangular( g,
                                             node.getXcoord(),
                                             new_x,
@@ -5428,6 +5422,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     private final void setupStroke( final Graphics2D g ) {
+        if ( getYdistance() < 0.0001 ) {
+            g.setStroke( STROKE_0025 );
+        }
         if ( getYdistance() < 0.001 ) {
             g.setStroke( STROKE_005 );
         }
@@ -5443,7 +5440,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else if ( getYdistance() < 2 ) {
             g.setStroke( STROKE_075 );
         }
-        else if ( getYdistance() < 20 ) {
+        else if ( ( getYdistance() < 20 ) || !getConfiguration().isAllowThickStrokes() ) {
             g.setStroke( STROKE_1 );
         }
         else {