inprogress

diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
index 2e2caf9..3309661 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -263,7 +263,6 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
 
     private final Phylogeny finishPhylogeny() throws PhylogenyParserException, NHXFormatException,
             PhyloXmlDataFormatException {
-        System.out.println( "finishPhylogeny()" + _current_phylogeny );
         if ( _current_phylogeny != null ) {
             parseNHX( _current_anotation != null ? _current_anotation.toString() : "",
                       _current_phylogeny.getRoot(),
@@ -281,6 +280,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
                     _current_phylogeny.setRooted( true );
                 }
             }
+            System.out.println( "finishPhylogeny()" + _current_phylogeny );
             return _current_phylogeny;
         }
         return null;
@@ -425,6 +425,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
             throw new PhylogenyParserException( "error in NH (Newick) formatted data: most likely cause: number of open parens does not equal number of close parens" );
         }
         if ( _current_phylogeny != null ) {
+            System.out.println( "getNext() going to call  finishPhylogeny()" );
             _next = finishPhylogeny();
             _current_phylogeny = null;
             _current_anotation = null;
@@ -507,6 +508,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
         final PhylogenyNode new_node = new PhylogenyNode();
         if ( _clade_level == 0 ) {
             if ( _current_phylogeny != null ) {
+                System.out.println( "processOpenParen() going to call  finishPhylogeny()" );
                 phy = finishPhylogeny();
             }
             _clade_level = 1;

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index e7aa418..d39c9ea 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -50,7 +50,6 @@ import org.forester.io.parsers.FastaParser;
 import org.forester.io.parsers.GeneralMsaParser;
 import org.forester.io.parsers.HmmscanPerDomainTableParser;
 import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
-import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
 import org.forester.io.parsers.nexus.NexusCharactersParser;
 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
@@ -407,14 +406,14 @@ public final class Test {
             String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
             final URL u = new URL( s );
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhylogenyParser parser = ParserUtils.createParserDependingOnUrlContents( u, true );
-            final Phylogeny[] phys = factory.create( u.openStream(), parser );
+            // final PhylogenyParser parser = new NHXParser();
+            final Phylogeny[] phys = factory.create( u.openStream(), new NHXParser() );
             System.out.println( "results 1:" );
             for( final Phylogeny phy : phys ) {
                 System.out.println( phy.toString() );
             }
             System.out.println( "" );
-            final Phylogeny[] phys3 = factory.create( "((a,b),c)", parser );
+            final Phylogeny[] phys3 = factory.create( "((a,b),c)", new NHXParser() );
             System.out.println( "results 3:" );
             for( final Phylogeny phy : phys3 ) {
                 System.out.println( phy.toString() );