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special domain coloring
[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 e8bbfea..df7306b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -173,6 +173,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     private static final BasicStroke     STROKE_2                                           = new BasicStroke( 2f );
     private static final double          TWO_PI                                             = 2 * Math.PI;
     private final static int             WIGGLE                                             = 2;
+    private static final String          SHOW_ONLY_THIS_CONF_TYPE                           = null;                                                     //TODO remove me
     HashMap<Long, Short>                 _nodeid_dist_to_leaf                               = new HashMap<Long, Short>();
     final private Arc2D                  _arc                                               = new Arc2D.Double();
     private AffineTransform              _at;
@@ -254,6 +255,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     private float                        _y_distance                                        = 0.0f;
     private int                          _length_of_longest_text;
     private int                          _longest_domain;
+    public final static boolean          SPECIAL_DOMAIN_COLORING                            = true;
     //  private Image                           offscreenImage;
     //  private Graphics                        offscreenGraphics;
     //  private Dimension                       offscreenDimension;
@@ -660,7 +662,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
                     && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
                 // FIXME 
-                sum += 100;
+                sum += RenderableMsaSequence.DEFAULT_WIDTH + 30;
             }
             if ( sum >= max_length ) {
                 _longest_ext_node_info = max_length;
@@ -1044,7 +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
@@ -1095,7 +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 {
@@ -2854,13 +2863,19 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
         if ( getFoundNodes0() != null ) {
             for( final Long id : getFoundNodes0() ) {
-                additional_nodes.add( _phylogeny.getNode( id ) );
+                final PhylogenyNode n = _phylogeny.getNode( id );
+                if ( n != null ) {
+                    additional_nodes.add( n );
+                }
             }
         }
         if ( getFoundNodes1() != null ) {
             for( final Long id : getFoundNodes1() ) {
                 if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) {
-                    additional_nodes.add( _phylogeny.getNode( id ) );
+                    final PhylogenyNode n = _phylogeny.getNode( id );
+                    if ( n != null ) {
+                        additional_nodes.add( n );
+                    }
                 }
             }
         }
@@ -4042,26 +4057,30 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         Collections.sort( confidences );
         final StringBuilder sb = new StringBuilder();
         for( final Confidence confidence : confidences ) {
-            final double value = confidence.getValue();
-            if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
-                if ( value < getOptions().getMinConfidenceValue() ) {
-                    return;
-                }
-                if ( not_first ) {
-                    sb.append( "/" );
-                }
-                else {
-                    not_first = true;
-                }
-                sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
-                        .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
-                if ( getOptions().isShowConfidenceStddev() ) {
-                    if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
-                        sb.append( "(" );
-                        sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
-                                                                                    getOptions()
-                                                                                            .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
-                        sb.append( ")" );
+            if ( ForesterUtil.isEmpty( SHOW_ONLY_THIS_CONF_TYPE )
+                    || ( !ForesterUtil.isEmpty( confidence.getType() ) && confidence.getType()
+                            .equalsIgnoreCase( SHOW_ONLY_THIS_CONF_TYPE ) ) ) {
+                final double value = confidence.getValue();
+                if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+                    if ( value < getOptions().getMinConfidenceValue() ) {
+                        return;
+                    }
+                    if ( not_first ) {
+                        sb.append( "/" );
+                    }
+                    else {
+                        not_first = true;
+                    }
+                    sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
+                            .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+                    if ( getOptions().isShowConfidenceStddev() ) {
+                        if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+                            sb.append( "(" );
+                            sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
+                                    .getStandardDeviation(), getOptions()
+                                    .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+                            sb.append( ")" );
+                        }
                     }
                 }
             }
@@ -4312,7 +4331,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
             return 0;
         }
-        if ( getOptions().isShowBranchLengthValues()
+        if ( getControlPanel().isWriteBranchLengthValues()
                 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
                         || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
                 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
@@ -4812,18 +4831,18 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         if ( getOptions().isRightLineUpDomains() ) {
                             rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
                                     + _length_of_longest_text + ( ( _longest_domain - rds.getTotalLength() ) * rds
-                                    .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2 ), g, this, to_pdf );
+                                    .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
                         }
                         else {
                             rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
-                                        node.getYcoord() - ( h / 2 ),
+                                        node.getYcoord() - ( h / 2.0f ),
                                         g,
                                         this,
                                         to_pdf );
                         }
                     }
                     else {
-                        rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2 ), g, this, to_pdf );
+                        rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
                     }
                 }
                 else {
@@ -4831,14 +4850,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text ) - 20 )
                                             + ( ( _longest_domain - rds.getTotalLength() ) * rds
                                                     .getRenderingFactorWidth() ),
-                                    node.getYcoord() - ( h / 2 ),
+                                    node.getYcoord() - ( h / 2.0f ),
                                     g,
                                     this,
                                     to_pdf );
                     }
                     else {
                         rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
-                                    node.getYcoord() - ( h / 2 ),
+                                    node.getYcoord() - ( h / 2.0f ),
                                     g,
                                     this,
                                     to_pdf );
@@ -4873,7 +4892,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
                 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
             final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence()
-                    .getMolecularSequence(), getConfiguration() );
+                    .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() );
             if ( rs != null ) {
                 final int default_height = 7;
                 float y = getYdistance();
@@ -4883,20 +4902,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height;
                 rs.setRenderingHeight( h > 1 ? h : 2 );
                 if ( getControlPanel().isDrawPhylogram() ) {
-                    if ( getOptions().isLineUpRendarableNodeData() ) {
-                        rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
-                                   node.getYcoord() - ( h / 2 ),
-                                   g,
-                                   this,
-                                   to_pdf );
-                    }
-                    else {
-                        rs.render( node.getXcoord() + x, node.getYcoord() - ( h / 2 ), g, this, to_pdf );
-                    }
+                    rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
+                               node.getYcoord() - ( h / 2.0f ),
+                               g,
+                               this,
+                               to_pdf );
                 }
                 else {
                     rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
-                               node.getYcoord() - ( h / 2 ),
+                               node.getYcoord() - ( h / 2.0f ),
                                g,
                                this,
                                to_pdf );