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bugfix
[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 bb31d7e..9e88db2 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 );
@@ -1637,14 +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()
+                    || ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() )
+                    || ( ( getFoundNodes1() != null ) && !getFoundNodes1().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 ) ) {
@@ -1988,16 +1995,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
 
     final void sortDescendants( final PhylogenyNode node ) {
         if ( !node.isExternal() ) {
-            DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
-            if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
-                    .isShowTaxonomyCommonNames() ) ) {
-                if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowSeqNames() || getControlPanel()
-                        .isShowSeqSymbols() ) ) {
-                    pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
-                }
-                else if ( getControlPanel().isShowNodeNames() ) {
-                    pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
-                }
+            DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
+            if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) {
+                pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
+            }
+            else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols()
+                    || getControlPanel().isShowGeneNames() ) {
+                pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
             }
             PhylogenyMethods.sortNodeDescendents( node, pri );
             setNodeInPreorderToNull();
@@ -2448,13 +2452,23 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else {
             fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
         }
-        fc.showDialog( this, "Select Font" );
-        if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
-            List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
-            if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
-                nodes = getFoundNodesAsListOfPhylogenyNodes();
-            }
+        List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+        if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+            nodes = getFoundNodesAsListOfPhylogenyNodes();
+        }
+        if ( !nodes.contains( node ) ) {
             nodes.add( node );
+        }
+        final int count = nodes.size();
+        String title = "Change the font for ";
+        if ( count == 1 ) {
+            title += "one node";
+        }
+        else {
+            title += ( count + " nodes" );
+        }
+        fc.showDialog( this, title );
+        if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
             for( final PhylogenyNode n : nodes ) {
                 if ( n.getNodeData().getNodeVisualData() == null ) {
                     n.getNodeData().setNodeVisualData( new NodeVisualData() );
@@ -2476,9 +2490,37 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 getControlPanel().getUseVisualStylesCb().setSelected( true );
             }
         }
+        setEdited( true );
         repaint();
     }
 
+    private void colorNodeFont( final PhylogenyNode node ) {
+        _color_chooser.setPreviewPanel( new JPanel() );
+        NodeColorizationActionListener al;
+        int count = 1;
+        if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+            final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+            al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
+            count = additional_nodes.size();
+            if ( !additional_nodes.contains( node ) ) {
+                count++;
+            }
+        }
+        else {
+            al = new NodeColorizationActionListener( _color_chooser, node );
+        }
+        String title = "Change the (node and font) color for ";
+        if ( count == 1 ) {
+            title += "one node";
+        }
+        else {
+            title += ( count + " nodes" );
+        }
+        final JDialog dialog = JColorChooser.createDialog( this, title, true, _color_chooser, al, null );
+        setEdited( true );
+        dialog.setVisible( true );
+    }
+
     final private void colorizeNodes( final Color c,
                                       final PhylogenyNode node,
                                       final List<PhylogenyNode> additional_nodes ) {
@@ -2519,20 +2561,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         repaint();
     }
 
-    private void colorNodeFont( final PhylogenyNode node ) {
-        _color_chooser.setPreviewPanel( new JPanel() );
-        NodeColorizationActionListener al;
-        if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
-            final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
-            al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
-        }
-        else {
-            al = new NodeColorizationActionListener( _color_chooser, node );
-        }
-        final JDialog dialog = JColorChooser.createDialog( this, "Node colorization", true, _color_chooser, al, null );
-        dialog.setVisible( true );
-    }
-
     final private void colorSubtree( final PhylogenyNode node ) {
         if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
             JOptionPane.showMessageDialog( this,
@@ -2552,6 +2580,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         final JDialog dialog = JColorChooser
                 .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
+        setEdited( true );
         dialog.setVisible( true );
     }
 
@@ -4705,7 +4734,8 @@ 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() ) ) {
@@ -4731,7 +4761,6 @@ 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 );
         float min_dist = 1.5f;
         if ( !disallow_shortcutting ) {
             if ( dynamic_hiding_factor > 4000 ) {
@@ -4773,7 +4802,7 @@ 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,
@@ -5415,6 +5444,9 @@ 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 );
         }
@@ -5430,7 +5462,7 @@ 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 {