fixing lining up of domains.

[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 b8905f2..18baad0 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -111,6 +111,7 @@ import org.forester.phylogeny.data.Accession;
 import org.forester.phylogeny.data.Annotation;
 import org.forester.phylogeny.data.BranchColor;
 import org.forester.phylogeny.data.Confidence;
+import org.forester.phylogeny.data.DomainArchitecture;
 import org.forester.phylogeny.data.Event;
 import org.forester.phylogeny.data.NodeData.NODE_DATA;
 import org.forester.phylogeny.data.NodeVisualData;
@@ -501,7 +502,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 calculateLongestExtNodeInfo();
                 if ( getOptions().isAllowFontSizeChange() ) {
                     if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
-                            && ( getTreeFontSet().getLargeFont().getSize() > 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
+                            && ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
                         while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) )
                                 && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
                             getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(),
@@ -511,8 +512,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     }
                     else {
                         while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
-                                && ( getTreeFontSet().getLargeFont().getSize() <= getTreeFontSet().getLargeFontMemory()
-                                        .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
+                                && ( getTreeFontSet().getLargeFont().getSize() <= ( getTreeFontSet()
+                                        .getLargeFontMemory().getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
                             getMainPanel().getTreeFontSet().increaseFontSize();
                             calculateLongestExtNodeInfo();
                         }
@@ -623,6 +624,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters()
                         .getGainedCharactersAsStringBuffer().toString() );
             }
+            if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
+                    && ( node.getNodeData().getVector().size() > 0 ) ) {
+                if ( getConfiguration() != null ) {
+                    sum += getConfiguration().getVectorDataWidth() + 10;
+                }
+                else {
+                    sum += RenderableVector.VECTOR_DEFAULT_WIDTH + 10;
+                }
+            }
+            if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
+                    && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+                // FIXME 
+                // TODO this might need some clean up
+                final DomainArchitecture d = node.getNodeData().getSequence().getDomainArchitecture();
+                sum += ( ( _domain_structure_width / ( ( RenderableDomainArchitecture ) d  ).getOriginalSize().getWidth() ) * d.getTotalLength() ) + 10;
+            }
             if ( sum >= max_length ) {
                 setLongestExtNodeInfo( max_length );
                 return;
@@ -716,6 +733,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
     }
 
+    final Color calculateSequenceBasedColor( final Sequence seq ) {
+        if ( ForesterUtil.isEmpty( seq.getName() ) ) {
+            return getTreeColorSet().getSequenceColor();
+        }
+        Color c = null;
+        final String seq_name = seq.getName();
+        c = getControlPanel().getSequenceColors().get( seq_name );
+        if ( c == null ) {
+            c = TreePanelUtil.calculateColorFromString( seq_name, false );
+            getControlPanel().getSequenceColors().put( seq_name, c );
+        }
+        return c;
+    }
+
     void checkForVectorProperties( final Phylogeny phy ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
@@ -986,12 +1017,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         return _statistics_for_vector_data;
     }
 
-    /**
-     * Find a color for this species name.
-     * 
-     * @param species
-     * @return the species color
-     */
     final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
         if ( node.getNodeData().isHasTaxonomy() ) {
             return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
@@ -1000,6 +1025,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         return getTreeColorSet().getTaxonomyColor();
     }
 
+    final Color getSequenceBasedColor( final PhylogenyNode node ) {
+        if ( node.getNodeData().isHasSequence() ) {
+            return calculateSequenceBasedColor( node.getNodeData().getSequence() );
+        }
+        // return non-colorized color
+        return getTreeColorSet().getSequenceColor();
+    }
+
     /**
      * @return pointer to colorset for tree drawing
      */
@@ -2450,8 +2483,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
         }
         if ( additional_nodes != null ) {
-            for( final PhylogenyNode n : additional_nodes ) {
-                n.getBranchData().setBranchColor( new BranchColor( c ) );
+            for( final PhylogenyNode an : additional_nodes ) {
+                for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) {
+                    it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+                }
             }
         }
         repaint();
@@ -2797,7 +2832,7 @@ 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() ) {
@@ -3924,6 +3959,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else if ( is_in_found_nodes ) {
             c = getColorForFoundNode( node );
         }
+        else if ( getControlPanel().isColorAccordingToSequence() ) {
+            c = getSequenceBasedColor( node );
+        }
         else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
             c = getTaxonomyBasedColor( node );
         }
@@ -3946,7 +3984,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             d = box_size;
         }
         final float xx = node.getXcoord() - ( 2 * box_size );
-        final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
+        final float xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1;
         _polygon.reset();
         _polygon.moveTo( xxx, node.getYcoord() );
         _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
@@ -4648,7 +4686,7 @@ 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 );
@@ -4723,7 +4761,7 @@ 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() ) ) {
@@ -4741,7 +4779,27 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 }
                 if ( rds != null ) {
                     rds.setRenderingHeight( 6 );
-                    rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
+                    if ( getControlPanel().isDrawPhylogram() ) {
+                        rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
+                    }
+                    else {
+                        int xx = 0;
+                        PhylogenyNode my_node = node;
+                        if ( !getControlPanel().isDrawPhylogram() ) {
+                            my_node = getPhylogeny().getFirstExternalNode();
+                        }
+                        if ( getControlPanel().isShowTaxonomyCode()
+                                && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
+                            xx += getFontMetricsForLargeDefaultFont()
+                                    .stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
+                        }
+                        if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
+                            //TODO fixme, need to look at all nodes not only the first
+                            xx += getFontMetricsForLargeDefaultFont().stringWidth( my_node.getName() + "      " );
+                        }
+                        //
+                        rds.render( my_node.getXcoord() + xx, node.getYcoord() - 3, g, this, to_pdf );
+                    }
                 }
             }
         }
@@ -5161,6 +5219,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 && ( node.getNodeData().getNodeVisualData().getFontColor() != null ) ) {
             g.setColor( node.getNodeData().getNodeVisualData().getFontColor() );
         }
+        else if ( getControlPanel().isColorAccordingToSequence() ) {
+            g.setColor( getSequenceBasedColor( node ) );
+        }
         else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
             g.setColor( getTaxonomyBasedColor( node ) );
         }
@@ -5689,9 +5750,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
                             _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
                         }
-                        else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
-                            _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
-                        }
                         else {
                             _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
                         }