in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 8832d0b..f53c94e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -43,7 +43,7 @@ public final class Constants {
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
     final static String         VERSION                                                       = "0.971 9M";
-    final static String         PRG_DATE                                                      = "2012.03.29";
+    final static String         PRG_DATE                                                      = "2012.04.09";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Verdana", "Tahoma",
             "Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index adb02a6..b58411b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -1715,7 +1715,8 @@ final class ControlPanel extends JPanel implements ActionListener {
         if ( _mainpanel.getCurrentScrollPane() == null ) {
             return;
         }
-        displayedPhylogenyMightHaveChanged( false );
+        getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
+        displayedPhylogenyMightHaveChanged( true );
         _mainpanel.getCurrentTreePanel().updateOvSettings();
         _mainpanel.getCurrentTreePanel().validate();
         _mainpanel.validate();
@@ -1815,7 +1816,7 @@ final class ControlPanel extends JPanel implements ActionListener {
                 node.setCollapse( false );
             }
             tp.resetNodeIdToDistToLeafMap();
-            tp.updateSetOfCollapsedExternalNodes( t );
+            tp.updateSetOfCollapsedExternalNodes();
             t.recalculateNumberOfExternalDescendants( false );
             tp.setNodeInPreorderToNull();
             t.hashIDs();

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index b1688a3..287a690 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -1113,7 +1113,7 @@ public final class MainFrameApplication extends MainFrame {
                 phy.hashIDs();
                 phy.recalculateNumberOfExternalDescendants( true );
                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
-                getCurrentTreePanel().updateSetOfCollapsedExternalNodes( phy );
+                getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
                 getCurrentTreePanel().calculateLongestExtNodeInfo();
                 getCurrentTreePanel().setNodeInPreorderToNull();
                 getCurrentTreePanel().recalculateMaxDistanceToRoot();

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 18d4089..c64a820 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -707,7 +707,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( !node.isExternal() && !node.isRoot() ) {
             final boolean collapse = !node.isCollapse();
             AptxUtil.collapseSubtree( node, collapse );
-            updateSetOfCollapsedExternalNodes( _phylogeny );
+            updateSetOfCollapsedExternalNodes();
             _phylogeny.recalculateNumberOfExternalDescendants( true );
             resetNodeIdToDistToLeafMap();
             calculateLongestExtNodeInfo();
@@ -726,7 +726,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         setWaitCursor();
         AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
-        updateSetOfCollapsedExternalNodes( _phylogeny );
+        updateSetOfCollapsedExternalNodes();
         _phylogeny.recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         calculateLongestExtNodeInfo();
@@ -2532,17 +2532,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
     }
 
-    void updateSetOfCollapsedExternalNodes( final Phylogeny phy ) {
+    void updateSetOfCollapsedExternalNodes() {
+        final Phylogeny phy = getPhylogeny();
         _collapsed_external_nodeid_set.clear();
-        E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
-            final PhylogenyNode ext_node = it.next();
-            PhylogenyNode n = ext_node;
-            while ( !n.isRoot() ) {
-                if ( n.isCollapse() ) {
-                    _collapsed_external_nodeid_set.add( ext_node.getId() );
-                    continue E;
-                }
-                n = n.getParent();
+        if ( phy != null ) {
+            E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+                final PhylogenyNode ext_node = it.next();
+                PhylogenyNode n = ext_node;
+                while ( !n.isRoot() ) {
+                    if ( n.isCollapse() ) {
+                        _collapsed_external_nodeid_set.add( ext_node.getId() );
+                        ext_node.setCollapse( true );
+                        continue E;
+                    }
+                    n = n.getParent();
+                }
             }
         }
     }

diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java b/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java
index c6a16f9..3a524bb 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java
@@ -27,29 +27,21 @@ package org.forester.io.parsers.nhx;
 
 public final class NHXtags {
 
-    public static final String CUSTOM_DATA_ON_NODE        = "XN=";
-    public static final String COLOR                      = "C=";
-    public static final String PARENT_BRANCH_WIDTH        = "W=";
-    public static final String SUBTREE_NEIGHBORS          = "SNn=";
-    public static final String SUPER_ORTHOLOGOUS          = "SOn=";
-    public static final String ORTHOLOGOUS                = "On=";
-    public static final String TAXONOMY_ID                = "T=";
-    public static final String SUPPORT                    = "B=";
-    public static final String IS_DUPLICATION             = "D=";
-    public static final String ANNOTATION                 = "AN="; //TODO fix on website NHXv2
-    public static final String SPECIES_NAME               = "S=";
-    public static final String DOMAIN_STRUCTURE           = "DS=";
-    public static final String GENE_NAME                  = "GN=";
-    public static final String GENE_NAME_SYNONYM          = "G=";
-    public static final String SEQUENCE_ACCESSION         = "AC=";
-    public static final String NODE_IDENTIFIER            = "ID="; //TODO fix on website NHXv2
-    public static final Object BRANCH_WIDTH               = "W=";
-    @Deprecated
-    public static final String BINARY_DOMAIN_COMBINATIONS = "GDC=";
-    @Deprecated
-    public static final String DOMAINS_SEPARATOR          = "\\|";
-    @Deprecated
-    public static final String DOMAINS                    = "GD=";
-    @Deprecated
-    public static final String EC_NUMBER                  = "E=";
+    public static final String CUSTOM_DATA_ON_NODE = "XN=";
+    public static final String COLOR               = "C=";
+    public static final String PARENT_BRANCH_WIDTH = "W=";
+    public static final String SUBTREE_NEIGHBORS   = "SNn=";
+    public static final String SUPER_ORTHOLOGOUS   = "SOn=";
+    public static final String ORTHOLOGOUS         = "On=";
+    public static final String TAXONOMY_ID         = "T=";
+    public static final String SUPPORT             = "B=";
+    public static final String IS_DUPLICATION      = "D=";
+    public static final String ANNOTATION          = "AN=";
+    public static final String SPECIES_NAME        = "S=";
+    public static final String DOMAIN_STRUCTURE    = "DS=";
+    public static final String GENE_NAME           = "GN=";
+    public static final String GENE_NAME_SYNONYM   = "G=";
+    public static final String SEQUENCE_ACCESSION  = "AC=";
+    public static final String NODE_IDENTIFIER     = "ID=";
+    public static final Object BRANCH_WIDTH        = "W=";
 }

diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
index 851398a..c4c5be2 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java
@@ -257,6 +257,12 @@ public final class PhyloXmlHandler extends DefaultHandler {
             }
             node.setDistanceToParent( d );
         }
+        if ( xml_element.isHasAttribute( PhyloXmlMapping.NODE_COLLAPSE ) ) {
+            final String collapse_str = xml_element.getAttribute( PhyloXmlMapping.NODE_COLLAPSE );
+            if ( !ForesterUtil.isEmpty( collapse_str ) && collapse_str.trim().equalsIgnoreCase( "true" ) ) {
+                node.setCollapse( true );
+            }
+        }
         for( int i = 0; i < xml_element.getNumberOfChildElements(); ++i ) {
             final XmlElement element = xml_element.getChildElement( i );
             final String qualified_name = element.getQualifiedName();

diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java
index 2a8d971..4659fc2 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java
@@ -42,6 +42,7 @@ public final class PhyloXmlMapping {
     public static final String PHYLOGENY_TYPE_ATTR                                 = "type";
     public static final String CLADE                                               = "clade";
     public static final String NODE_NAME                                           = "name";
+    public static final String NODE_COLLAPSE                                       = "collapse";
     public static final String SEQUENCE                                            = "sequence";
     public static final String SEQUENCE_NAME                                       = "name";
     public static final String SEQUENCE_SYMBOL                                     = "symbol";

diff --git a/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java b/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java
index 5860cac..67d38d4 100644 (file)
--- a/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java
+++ b/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java
@@ -39,7 +39,7 @@ public class PhyloXmlNodeWriter {
     public static void toPhyloXml( final Writer w, final PhylogenyNode node, final int level, final String indentation )
             throws IOException {
         String ind = "";
-        if ( indentation.length() > 0 ) {
+        if ( ( indentation != null ) && ( indentation.length() > 0 ) ) {
             ind = indentation + PhylogenyWriter.PHYLO_XML_INTENDATION_BASE;
         }
         if ( !ForesterUtil.isEmpty( node.getName() ) ) {

diff --git a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
index b41d8d7..36dfda4 100644 (file)
--- a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
+++ b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
@@ -552,12 +552,10 @@ public final class PhylogenyWriter {
                 }
                 PhylogenyDataUtil.appendOpen( getWriter(), PhyloXmlMapping.CLADE );
             }
-            if ( indentation != null ) {
-                PhyloXmlNodeWriter.toPhyloXml( getWriter(), node, getPhyloXmlLevel(), indentation.toString() );
-            }
-            else {
-                PhyloXmlNodeWriter.toPhyloXml( getWriter(), node, getPhyloXmlLevel(), "" );
-            }
+            PhyloXmlNodeWriter.toPhyloXml( getWriter(),
+                                           node,
+                                           getPhyloXmlLevel(),
+                                           indentation != null ? indentation.toString() : "" );
             if ( node.isExternal() ) {
                 getWriter().write( ForesterUtil.LINE_SEPARATOR );
                 if ( indentation != null ) {
@@ -594,7 +592,15 @@ public final class PhylogenyWriter {
                 if ( isIndentPhyloxml() ) {
                     getWriter().write( createIndentation().toString() );
                 }
-                PhylogenyDataUtil.appendOpen( getWriter(), PhyloXmlMapping.CLADE );
+                if ( node.isCollapse() ) {
+                    PhylogenyDataUtil.appendOpen( getWriter(),
+                                                  PhyloXmlMapping.CLADE,
+                                                  PhyloXmlMapping.NODE_COLLAPSE,
+                                                  "true" );
+                }
+                else {
+                    PhylogenyDataUtil.appendOpen( getWriter(), PhyloXmlMapping.CLADE );
+                }
             }
             else if ( ( getOutputFormt() == FORMAT.NHX ) || ( getOutputFormt() == FORMAT.NH ) ) {
                 getBuffer().append( "(" );