testing under java 8...

once again stream closed issues...

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 4bcfb08..7a30ce9 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -127,10 +127,10 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
     @Override
     public final Phylogeny[] parse() throws IOException {
         final List<Phylogeny> l = new ArrayList<Phylogeny>();
-        int c = 0;
+        //int c = 0;
         while ( hasNext() ) {
             l.add( next() );
-            c++;
+           // c++;
         }
         final Phylogeny[] p = new Phylogeny[ l.size() ];
         for( int i = 0; i < l.size(); ++i ) {
@@ -158,7 +158,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
         _my_source_sbuff = null;
         _my_source_sbuil = null;
         _my_source_charary = null;
-        determineSourceType( _source );
+        determineAndProcessSourceType( _source );
         switch ( _input_type ) {
             case STRING:
                 _my_source_br = null;
@@ -211,7 +211,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
         _allow_errors_in_distance_to_parent = allow_errors_in_distance_to_parent;
     }
 
-    private final void determineSourceType( final Object nhx_source ) throws IOException {
+    private final void determineAndProcessSourceType( final Object nhx_source ) throws IOException {
         if ( nhx_source == null ) {
             throw new PhylogenyParserException( getClass() + ": attempt to parse null object." );
         }
@@ -244,11 +244,12 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
             _input_type = NHXParser.BUFFERED_READER;
             _source_length = 0;
             if ( _my_source_br != null ) {
-                try {
-                    _my_source_br.close();
-                }
-                catch ( final IOException e ) {
-                }
+             // I am REALLY not sure if it a "good" NOT to close the stream... 
+//                try {
+//                    _my_source_br.close();
+//                }
+//                catch ( final IOException e ) {
+//                }
             }
             final File f = ( File ) nhx_source;
             final String error = ForesterUtil.isReadableFile( f );
@@ -261,11 +262,12 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
             _input_type = NHXParser.BUFFERED_READER;
             _source_length = 0;
             if ( _my_source_br != null ) {
-                try {
-                    _my_source_br.close();
-                }
-                catch ( final IOException e ) {
-                }
+// I am REALLY not sure if it a "good" NOT to close the stream...                
+//                try {
+//                    _my_source_br.close();
+//                }
+//                catch ( final IOException e ) {
+//                }
             }
             final InputStreamReader isr = new InputStreamReader( ( ( URL ) nhx_source ).openStream() );
             _nhx_source = new BufferedReader( isr );
@@ -274,11 +276,12 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
             _input_type = NHXParser.BUFFERED_READER;
             _source_length = 0;
             if ( _my_source_br != null ) {
-                try {
-                    _my_source_br.close();
-                }
-                catch ( final IOException e ) {
-                }
+             // I am REALLY not sure if it a "good" NOT to close the stream...   
+//                try {
+//                    _my_source_br.close();
+//                }
+//                catch ( final IOException e ) {
+//                }
             }
             final InputStreamReader isr = new InputStreamReader( ( InputStream ) nhx_source );
             _nhx_source = new BufferedReader( isr );

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index feddccc..713d018 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -139,7 +139,7 @@ public final class Test {
     private final static String  PATH_TO_TEST_DATA         = System.getProperty( "user.dir" )
                                                                    + ForesterUtil.getFileSeparator() + "test_data"
                                                                    + ForesterUtil.getFileSeparator();
-    private final static boolean PERFORM_DB_TESTS          = true;
+    private final static boolean PERFORM_DB_TESTS          = false;
     private static final boolean PERFORM_WEB_TREE_ACCESS   = true;
     private static final String  PHYLOXML_LOCAL_XSD        = PATH_TO_RESOURCES + "phyloxml_schema/"
                                                                    + ForesterConstants.PHYLO_XML_VERSION + "/"
@@ -181,6 +181,22 @@ public final class Test {
             System.exit( -1 );
         }
         final long start_time = new Date().getTime();
+        
+        //
+        if ( Test.testNHXparsingFromURL() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
+       // System.exit( 1 );
+        
+        //
+        
+        
+        
         System.out.print( "MSA entropy: " );
         if ( Test.testMsaEntropy() ) {
             System.out.println( "OK." );
@@ -1218,6 +1234,7 @@ public final class Test {
         }
         catch ( final Exception e ) {
             e.printStackTrace();
+            return false;
         }
         return true;
     }
@@ -1239,7 +1256,10 @@ public final class Test {
                 System.out.println( phys[ 1 ].toNewHampshire() );
                 return false;
             }
-            final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() );
+            
+            final URL u2 = new URL( s );
+            
+            final Phylogeny[] phys2 = factory.create( u2.openStream(), new NHXParser() );
             if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
                 return false;
             }
@@ -1249,8 +1269,8 @@ public final class Test {
             }
             final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
             final NHXParser p = new NHXParser();
-            final URL u2 = new URL( s );
-            p.setSource( u2 );
+            final URL u3 = new URL( s );
+            p.setSource( u3 );
             if ( !p.hasNext() ) {
                 return false;
             }
@@ -1282,7 +1302,9 @@ public final class Test {
             }
         }
         catch ( final Exception e ) {
+            System.out.println( e.toString());
             e.printStackTrace();
+            return false;
         }
         return true;
     }