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 ce136b5..15fe777 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -136,6 +136,7 @@ import org.forester.util.TaxonomyUtil;
 
 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
 
+    public final static boolean          SPECIAL_DOMAIN_COLORING                            = true;
     final static Cursor                  ARROW_CURSOR                                       = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
     final static Cursor                  CUT_CURSOR                                         = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
     final static Cursor                  HAND_CURSOR                                        = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
@@ -1045,7 +1046,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
-        if ( node.getNodeData().isHasTaxonomy() ) {
+        if ( node.isExternal() && node.getNodeData().isHasTaxonomy() ) {
             return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
         }
         // return non-colorized color
@@ -1096,7 +1097,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
                 RenderableDomainArchitecture rds = null;
                 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
-                    rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture() );
+                    if ( SPECIAL_DOMAIN_COLORING ) {
+                        rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
+                                .getDomainArchitecture(), node.getName() );
+                    }
+                    else {
+                        rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
+                                .getDomainArchitecture() );
+                    }
                     node.getNodeData().getSequence().setDomainArchitecture( rds );
                 }
                 else {
@@ -1629,14 +1637,20 @@ 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 ) ) {
@@ -1980,16 +1994,13 @@ 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();
@@ -2468,6 +2479,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 getControlPanel().getUseVisualStylesCb().setSelected( true );
             }
         }
+        setEdited( true );
         repaint();
     }
 
@@ -2522,6 +2534,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             al = new NodeColorizationActionListener( _color_chooser, node );
         }
         final JDialog dialog = JColorChooser.createDialog( this, "Node colorization", true, _color_chooser, al, null );
+        setEdited( true );
         dialog.setVisible( true );
     }
 
@@ -2544,6 +2557,7 @@ 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 );
     }
 
@@ -4158,6 +4172,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
                 || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
                 || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
+                || ( getOptions().isShowDefaultNodeShapesForMarkedNodes()
+                        && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData()
+                        .getNodeVisualData().isEmpty() ) )
                 || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node
                         .getNodeData().getNodeVisualData().getNodeColor() != null )
                         || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )
@@ -4694,7 +4711,8 @@ 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() ) ) {
@@ -4720,7 +4738,6 @@ 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 ) {
@@ -4762,7 +4779,7 @@ 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,