From: cmzmasek <cmzmasek@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 18 Feb 2014 02:27:58 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=df699a17e2a746285c79127645458d98e6e4a9be;p=jalview.git

in progress
---

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 3309661..b2543a0 100644
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -114,24 +114,26 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
     public final Phylogeny next() throws NHXFormatException, IOException {
         final Phylogeny phy = _next;
         getNext();
+       
         return phy;
     }
 
     @Override
     public final Phylogeny[] parse() throws IOException {
-        reset();
+    
         final List<Phylogeny> l = new ArrayList<Phylogeny>();
+        int c = 0;
         while ( hasNext() ) {
+           
             l.add( next() );
+            c++;
         }
         final Phylogeny[] p = new Phylogeny[ l.size() ];
         for( int i = 0; i < l.size(); ++i ) {
             p[ i ] = l.get( i );
         }
-        System.out.println( "going to return:" );
-        for( Phylogeny phylogeny : p ) {
-            System.out.println( phylogeny.toString() );
-        }
+    
+        reset();
         return p;
     }
 
@@ -280,7 +282,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
                     _current_phylogeny.setRooted( true );
                 }
             }
-            System.out.println( "finishPhylogeny()" + _current_phylogeny );
+        
             return _current_phylogeny;
         }
         return null;
@@ -331,7 +333,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
                     }
                 }
             }
-            System.out.print( c );
+       
             if ( !_in_single_quote && !_in_double_quote ) {
                 if ( c == ':' ) {
                     _saw_colon = true;
@@ -425,7 +427,7 @@ 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;
@@ -508,7 +510,7 @@ 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 d39c9ea..08ae65e 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -401,28 +401,43 @@ public final class Test {
         return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
     }
 
-    public static void main( final String[] args ) {
+    
+    public static final boolean testNHXparsingFromURL() {
         try {
             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 = 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() );
+           
+           
+            if ( phys == null || phys.length != 1  ) {
+                return false;
+                
             }
-            System.out.println( "" );
-            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() );
+            if ( !phys[ 0 ].toNewHampshire().equals( "((a,b),c);" ) ) {
+                System.out.println(phys[ 0 ].toNewHampshire() );
+                return false;
+            }
+            
+            final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() );
+            if ( phys2 == null || phys2.length != 1  ) {
+                return false;
+                
+            }
+            if ( !phys2[ 0 ].toNewHampshire().equals( "((a,b),c);" ) ) {
+                System.out.println(phys2[ 0 ].toNewHampshire() );
+                return false;
             }
         }
         catch ( Exception e ) {
             e.printStackTrace();
         }
-        System.exit( 0 );
+        return true;
+    }
+    
+    public static void main( final String[] args ) {
+       
+     
         System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
         System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
                 + "]" );
@@ -1223,6 +1238,18 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
+        
+       
+        System.out.print( "NHX parsing from URL: " );
+        if ( Test.testNHXparsingFromURL() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
+        
         System.out.println();
         final Runtime rt = java.lang.Runtime.getRuntime();
         final long free_memory = rt.freeMemory() / 1000000;