X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=3f6496b657801c77783c5e3133584ce84d1e54c3;hb=825120e331e7944f5f2498e72c58402f5fc6442a;hp=a4c7821c9cf4048e80a6d45dfd33f3d8e70c529a;hpb=7e567e18a5ba32035a8db4ca041023c9e862d25b;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index a4c7821..3f6496b 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -98,6 +98,7 @@ import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
+import org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence;
 import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
 import org.forester.archaeopteryx.tools.Blast;
 import org.forester.archaeopteryx.tools.ImageLoader;
@@ -655,6 +656,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     _longest_domain = d.getTotalLength();
                 }
             }
+            if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
+                    && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
+                    && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
+                // FIXME 
+                sum += RenderableMsaSequence.DEFAULT_WIDTH + 30;
+            }
             if ( sum >= max_length ) {
                 _longest_ext_node_info = max_length;
                 return;
@@ -1103,7 +1110,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
         }
         if ( getControlPanel().isShowDomainArchitectures() ) {
-            final double ds_factor_width = _domain_structure_width / _max_original_domain_structure_width;
+            final float ds_factor_width = ( float ) ( _domain_structure_width / _max_original_domain_structure_width );
             for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
                 if ( node.getNodeData().isHasSequence()
                         && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
@@ -3426,48 +3433,53 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) {
-        if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
-            if ( sb.length() > 0 ) {
-                sb.append( " " );
-            }
-            sb.append( node.getName() );
-        }
-        if ( node.getNodeData().isHasSequence() ) {
-            if ( getControlPanel().isShowSeqSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
+        if ( node != null ) {
+            if ( getControlPanel().isShowNodeNames() && ( !ForesterUtil.isEmpty( node.getName() ) ) ) {
                 if ( sb.length() > 0 ) {
                     sb.append( " " );
                 }
-                sb.append( node.getNodeData().getSequence().getSymbol() );
+                sb.append( node.getName() );
             }
-            if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
-                if ( sb.length() > 0 ) {
-                    sb.append( " " );
+            if ( node.getNodeData().isHasSequence() ) {
+                if ( getControlPanel().isShowSeqSymbols()
+                        && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
+                    if ( sb.length() > 0 ) {
+                        sb.append( " " );
+                    }
+                    sb.append( node.getNodeData().getSequence().getSymbol() );
                 }
-                sb.append( node.getNodeData().getSequence().getGeneName() );
-            }
-            if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
-                if ( sb.length() > 0 ) {
-                    sb.append( " " );
+                if ( getControlPanel().isShowGeneNames()
+                        && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+                    if ( sb.length() > 0 ) {
+                        sb.append( " " );
+                    }
+                    sb.append( node.getNodeData().getSequence().getGeneName() );
+                }
+                if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+                    if ( sb.length() > 0 ) {
+                        sb.append( " " );
+                    }
+                    sb.append( node.getNodeData().getSequence().getName() );
+                }
+                if ( getControlPanel().isShowSequenceAcc()
+                        && ( node.getNodeData().getSequence().getAccession() != null ) ) {
+                    if ( sb.length() > 0 ) {
+                        sb.append( " " );
+                    }
+                    if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
+                        sb.append( node.getNodeData().getSequence().getAccession().getSource() );
+                        sb.append( ":" );
+                    }
+                    sb.append( node.getNodeData().getSequence().getAccession().getValue() );
                 }
-                sb.append( node.getNodeData().getSequence().getName() );
             }
-            if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
+            if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
                 if ( sb.length() > 0 ) {
                     sb.append( " " );
                 }
-                if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
-                    sb.append( node.getNodeData().getSequence().getAccession().getSource() );
-                    sb.append( ":" );
-                }
-                sb.append( node.getNodeData().getSequence().getAccession().getValue() );
+                sb.append( propertiesToString( node ) );
             }
         }
-        if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
-            if ( sb.length() > 0 ) {
-                sb.append( " " );
-            }
-            sb.append( propertiesToString( node ) );
-        }
     }
 
     private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) {
@@ -4778,7 +4790,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             return;
         }
         if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
-                && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+                && ( node.getNodeData().getSequence().getDomainArchitecture() != null )
+                && ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
             RenderableDomainArchitecture rds = null;
             try {
                 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
@@ -4797,17 +4810,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 if ( getControlPanel().isDrawPhylogram() ) {
                     if ( getOptions().isLineUpRendarableNodeData() ) {
                         if ( getOptions().isRightLineUpDomains() ) {
-                            rds.render( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
-                                                + _length_of_longest_text
-                                                + ( ( _longest_domain - rds.getTotalLength() ) * rds
-                                                        .getRenderingFactorWidth() ),
-                                        node.getYcoord() - ( h / 2 ),
-                                        g,
-                                        this,
-                                        to_pdf );
+                            rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+                                    + _length_of_longest_text + ( ( _longest_domain - rds.getTotalLength() ) * rds
+                                    .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2 ), g, this, to_pdf );
                         }
                         else {
-                            rds.render( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text,
+                            rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
                                         node.getYcoord() - ( h / 2 ),
                                         g,
                                         this,
@@ -4850,10 +4858,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     domain_add = _domain_structure_width + 10;
                 }
                 if ( getControlPanel().isDrawPhylogram() ) {
-                    rv.render( node.getXcoord() + x + domain_add, node.getYcoord() - 3, g, this, to_pdf );
+                    rv.render( ( float ) ( node.getXcoord() + x + domain_add ), node.getYcoord() - 3, g, this, to_pdf );
                 }
                 else {
-                    rv.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text + domain_add,
+                    rv.render( ( float ) ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text + domain_add ),
                                node.getYcoord() - 3,
                                g,
                                this,
@@ -4861,13 +4869,47 @@ 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(), 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 ),
+                                   g,
+                                   this,
+                                   to_pdf );
+                    
+                    
+                }
+                else {
+                    rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
+                               node.getYcoord() - ( h / 2 ),
+                               g,
+                               this,
+                               to_pdf );
+                }
+            }
+        }
     }
 
     final private int calcLengthOfLongestText() {
         final StringBuilder sb = new StringBuilder();
-        nodeDataAsSB( _ext_node_with_longest_txt_info, sb );
-        if ( _ext_node_with_longest_txt_info.getNodeData().isHasTaxonomy() ) {
-            nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb );
+        if ( _ext_node_with_longest_txt_info != null ) {
+            nodeDataAsSB( _ext_node_with_longest_txt_info, sb );
+            if ( _ext_node_with_longest_txt_info.getNodeData().isHasTaxonomy() ) {
+                nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb );
+            }
         }
         return getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
     }