in progress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrameApplication.java

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