X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=38afbce942c16853aa662c5156c9cf25005747e5;hb=046e97b211db481219195ad13875ad03ddc2225d;hp=d0d6ddc1b5f0e8e62064c65d461896648302a1e7;hpb=09028c5abedb9492d6fc76b4274f6dd46bcf6cd6;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index d0d6ddc..38afbce 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -176,7 +176,7 @@ 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                           = "posterior probability";                                  //TODO remove me
+    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;
@@ -4790,6 +4790,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file );
         }
+        if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
+                && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
+                && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
+            paintMolecularSequences( g, node, to_pdf );
+        }
         if ( dynamically_hide
                 && !is_in_found_nodes
                 && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
@@ -4892,33 +4897,37 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 }
             }
         }
-        if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
-                && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
-                && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
-            final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence()
-                                                                                   .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() );
-            if ( rs != null ) {
-                final int default_height = 7;
-                float y = getYdistance();
-                if ( getControlPanel().isDynamicallyHideData() ) {
-                    y = getTreeFontSet().getFontMetricsLarge().getHeight();
-                }
-                final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height;
-                rs.setRenderingHeight( h > 1 ? h : 2 );
-                if ( getControlPanel().isDrawPhylogram() ) {
-                    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 / 2.0f ),
-                               g,
-                               this,
-                               to_pdf );
-                }
+       
+        //if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
+        //        && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
+        //        && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
+        //    paintMolecularSequences( g, node, to_pdf );
+        //}
+    }
+
+    private void paintMolecularSequences( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf ) {
+        final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence()
+                                                                               .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() );
+        if ( rs != null ) {
+            final int default_height = 8;
+            float y = getYdistance();
+           
+            final int h = ( y / 2) < default_height ? ForesterUtil.roundToInt( y * 2 ) : default_height;
+            rs.setRenderingHeight( h > 1 ? h : 1 );
+           
+            if ( getControlPanel().isDrawPhylogram() ) {
+                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 / 2.0f ),
+                           g,
+                           this,
+                           to_pdf );
             }
         }
     }