X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fwriters%2FPhylogenyWriter.java;h=b41d8d7d60b6f4e2567bfef89d67899d45347810;hb=780b50a029ad352bd7b309eab711c48c6bce3ef0;hp=c443842db2bc10396454adf17eee56553f32f3c9;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
index c443842..b41d8d7 100644
--- a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
+++ b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
@@ -41,6 +41,7 @@ import org.forester.io.parsers.nexus.NexusConstants;
 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PostOrderStackObject;
@@ -73,6 +74,7 @@ public final class PhylogenyWriter {
     private Stack<PostOrderStackObject> _stack;
     private boolean                     _simple_nh;
     private boolean                     _nh_write_distance_to_parent;
+    NH_CONVERSION_SUPPORT_VALUE_STYLE   _nh_conversion_support_style;
     private boolean                     _indent_phyloxml;
     private int                         _node_level;
     private int                         _phyloxml_level;
@@ -80,6 +82,7 @@ public final class PhylogenyWriter {
 
     public PhylogenyWriter() {
         setIndentPhyloxml( INDENT_PHYLOXML_DEAFULT );
+        setNhConversionSupportStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
     }
 
     private void appendPhylogenyLevelPhyloXml( final Writer writer, final Phylogeny tree ) throws IOException {
@@ -336,6 +339,17 @@ public final class PhylogenyWriter {
 
     public StringBuffer toNewHampshire( final Phylogeny tree,
                                         final boolean simple_nh,
+                                        final boolean nh_write_distance_to_parent,
+                                        final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) throws IOException {
+        setOutputFormt( FORMAT.NH );
+        setNhConversionSupportStyle( svs );
+        setSimpleNH( simple_nh );
+        setWriteDistanceToParentInNH( nh_write_distance_to_parent );
+        return getOutput( tree );
+    }
+
+    public StringBuffer toNewHampshire( final Phylogeny tree,
+                                        final boolean simple_nh,
                                         final boolean nh_write_distance_to_parent ) throws IOException {
         setOutputFormt( FORMAT.NH );
         setSimpleNH( simple_nh );
@@ -350,6 +364,14 @@ public final class PhylogenyWriter {
         writeToFile( toNewHampshire( tree, simple_nh, write_distance_to_parent ), out_file );
     }
 
+    public void toNewHampshire( final Phylogeny tree,
+                                final boolean simple_nh,
+                                final boolean write_distance_to_parent,
+                                final NH_CONVERSION_SUPPORT_VALUE_STYLE svs,
+                                final File out_file ) throws IOException {
+        writeToFile( toNewHampshire( tree, simple_nh, write_distance_to_parent, svs ), out_file );
+    }
+
     public void toNewHampshire( final Phylogeny[] trees,
                                 final boolean simple_nh,
                                 final boolean write_distance_to_parent,
@@ -393,34 +415,26 @@ public final class PhylogenyWriter {
         writeToFile( sb, out_file );
     }
 
-    public void toNexus( final File out_file, final List<Phylogeny> trees ) throws IOException {
-        final Writer writer = new BufferedWriter( new PrintWriter( out_file ) );
-        writeNexusStart( writer );
-        writeNexusTaxaBlock( writer, trees.get( 0 ) );
-        writeNexusTreesBlock( writer, trees );
-        writer.flush();
-        writer.close();
-    }
-
-    public void toNexus( final File out_file, final Phylogeny tree ) throws IOException {
+    public void toNexus( final File out_file, final Phylogeny tree, final NH_CONVERSION_SUPPORT_VALUE_STYLE svs )
+            throws IOException {
         final Writer writer = new BufferedWriter( new PrintWriter( out_file ) );
         final List<Phylogeny> trees = new ArrayList<Phylogeny>( 1 );
         trees.add( tree );
         writeNexusStart( writer );
         writeNexusTaxaBlock( writer, tree );
-        writeNexusTreesBlock( writer, trees );
+        writeNexusTreesBlock( writer, trees, svs );
         writer.flush();
         writer.close();
     }
 
-    public StringBuffer toNexus( final Phylogeny tree ) throws IOException {
+    public StringBuffer toNexus( final Phylogeny tree, final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) throws IOException {
         final StringWriter string_writer = new StringWriter();
         final Writer writer = new BufferedWriter( string_writer );
         final List<Phylogeny> trees = new ArrayList<Phylogeny>( 1 );
         trees.add( tree );
         writeNexusStart( writer );
         writeNexusTaxaBlock( writer, tree );
-        writeNexusTreesBlock( writer, trees );
+        writeNexusTreesBlock( writer, trees, svs );
         writer.flush();
         writer.close();
         return string_writer.getBuffer();
@@ -556,10 +570,20 @@ public final class PhylogenyWriter {
             getBuffer().append( node.toNewHampshireX() );
         }
         else if ( getOutputFormt() == FORMAT.NH ) {
-            getBuffer().append( node.toNewHampshire( isSimpleNH(), isWriteDistanceToParentInNH() ) );
+            getBuffer().append( node.toNewHampshire( isSimpleNH(),
+                                                     isWriteDistanceToParentInNH(),
+                                                     getNhConversionSupportStyle() ) );
         }
     }
 
+    private NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportStyle() {
+        return _nh_conversion_support_style;
+    }
+
+    private void setNhConversionSupportStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
+        _nh_conversion_support_style = nh_conversion_support_style;
+    }
+
     private void writeOpenClade( final PhylogenyNode node ) throws IOException {
         if ( !isSawComma() ) {
             if ( !node.isRoot() && node.isFirstChildNode() ) {
@@ -711,7 +735,9 @@ public final class PhylogenyWriter {
         writer.write( ForesterUtil.LINE_SEPARATOR );
     }
 
-    public static void writeNexusTreesBlock( final Writer writer, final List<Phylogeny> trees ) throws IOException {
+    public static void writeNexusTreesBlock( final Writer writer,
+                                             final List<Phylogeny> trees,
+                                             final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) throws IOException {
         writer.write( NexusConstants.BEGIN_TREES );
         writer.write( ForesterUtil.LINE_SEPARATOR );
         int i = 1;
@@ -735,7 +761,7 @@ public final class PhylogenyWriter {
             else {
                 writer.write( "[&U]" );
             }
-            writer.write( phylogeny.toNewHampshire( false ) );
+            writer.write( phylogeny.toNewHampshire( false, svs ) );
             writer.write( ForesterUtil.LINE_SEPARATOR );
             i++;
         }