X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=85e93363a49a8b8735e7ddc40b7b4165944d5069;hb=f642399d323502c48c4ccb25ad6a4268a4152e6a;hp=947ed2ace1f23fe877e8e7e18cf9a477554d87ba;hpb=6b3ec0cd978bd692dfae1de3e076963283fdf322;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 947ed2a..85e9336 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -93,6 +93,7 @@ import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.Confidence;
+import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
@@ -123,6 +124,7 @@ public final class MainFrameApplication extends MainFrame {
     private final static SequencesFileFilter seqsfilter                            = new SequencesFileFilter();
     private final static DefaultFilter       defaultfilter                         = new DefaultFilter();
     private static final long                serialVersionUID                      = -799735726778865234L;
+    private static final boolean             PREPROCESS_TREES                      = false;
     private final JFileChooser               _values_filechooser;
     private final JFileChooser               _sequences_filechooser;
     private final JFileChooser               _open_filechooser;
@@ -896,11 +898,11 @@ public final class MainFrameApplication extends MainFrame {
                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
         _options_jmenu
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
+        _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
-            _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
+            _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
         }
-        _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
         _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
@@ -2211,6 +2213,9 @@ public final class MainFrameApplication extends MainFrame {
                                 }
                             }
                         }
+                        if ( PREPROCESS_TREES ) {
+                            preProcessTreesUponReading( phys );
+                        }
                         AptxUtil.addPhylogeniesToTabs( phys,
                                                        file.getName(),
                                                        file.getAbsolutePath(),
@@ -2234,6 +2239,30 @@ public final class MainFrameApplication extends MainFrame {
         System.gc();
     }
 
+    private void preProcessTreesUponReading( final Phylogeny[] phys ) {
+        for( final Phylogeny phy : phys ) {
+            if ( ( phy != null ) && !phy.isEmpty() ) {
+                for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
+                    final PhylogenyNode n = it.next();
+                    if ( n.isExternal() ) {
+                        if ( n.getNodeData().isHasSequence() ) {
+                            final Sequence s = n.getNodeData().getSequence();
+                            if ( ForesterUtil.isEmpty( s.getGeneName() ) ) {
+                                if ( ( s.getAccession() != null )
+                                        && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {
+                                    s.setGeneName( s.getAccession().getValue() );
+                                }
+                                else if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+                                    s.setGeneName( n.getName() );
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+
     private void readSpeciesTreeFromFile() {
         Phylogeny t = null;
         boolean exception = false;