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 b2543a0..daf3360 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -113,18 +113,15 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
     @Override
     public final Phylogeny next() throws NHXFormatException, IOException {
         final Phylogeny phy = _next;
-        getNext();
-       
+        parseNext();
         return phy;
     }
 
     @Override
     public final Phylogeny[] parse() throws IOException {
-    
         final List<Phylogeny> l = new ArrayList<Phylogeny>();
         int c = 0;
         while ( hasNext() ) {
-           
             l.add( next() );
             c++;
         }
@@ -132,7 +129,6 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
         for( int i = 0; i < l.size(); ++i ) {
             p[ i ] = l.get( i );
         }
-    
         reset();
         return p;
     }
@@ -185,7 +181,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
             default:
                 throw new RuntimeException( "unknown input type" );
         }
-        getNext();
+        parseNext();
     }
 
     public final void setGuessRootedness( final boolean guess_rootedness ) {
@@ -282,7 +278,6 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
                     _current_phylogeny.setRooted( true );
                 }
             }
-        
             return _current_phylogeny;
         }
         return null;
@@ -297,7 +292,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
         return _current_phylogeny;
     }
 
-    private final void getNext() throws IOException, NHXFormatException {
+    private final void parseNext() throws IOException, NHXFormatException {
         if ( _source == null ) {
             throw new IOException( "source is not set" );
         }
@@ -333,7 +328,6 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
                     }
                 }
             }
-       
             if ( !_in_single_quote && !_in_double_quote ) {
                 if ( c == ':' ) {
                     _saw_colon = true;
@@ -427,7 +421,6 @@ 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 ) {
-          
             _next = finishPhylogeny();
             _current_phylogeny = null;
             _current_anotation = null;
@@ -510,7 +503,6 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
         final PhylogenyNode new_node = new PhylogenyNode();
         if ( _clade_level == 0 ) {
             if ( _current_phylogeny != null ) {
-             
                 phy = finishPhylogeny();
             }
             _clade_level = 1;
@@ -713,6 +705,16 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
         }
     }
 
+    public final static NHXParser createInstance( final Object nhx_source ) throws NHXFormatException, IOException {
+        final NHXParser parser = new NHXParser();
+        parser.setSource( nhx_source );
+        return parser;
+    }
+
+    public final static Phylogeny[] parse( final Object nhx_source ) throws NHXFormatException, IOException {
+        return NHXParser.createInstance( nhx_source ).parse();
+    }
+
     @Override
     public String getName() {
         return "NN/NHX Parser";

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 08ae65e..629eb44 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -401,43 +401,35 @@ public final class Test {
         return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
     }
 
-    
     public static final boolean testNHXparsingFromURL() {
         try {
-            String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
+            final 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 Phylogeny[] phys = factory.create( u.openStream(), new NHXParser() );
-           
-           
-            if ( phys == null || phys.length != 1  ) {
+            if ( ( phys == null ) || ( phys.length != 1 ) ) {
                 return false;
-                
             }
             if ( !phys[ 0 ].toNewHampshire().equals( "((a,b),c);" ) ) {
-                System.out.println(phys[ 0 ].toNewHampshire() );
+                System.out.println( phys[ 0 ].toNewHampshire() );
                 return false;
             }
-            
             final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() );
-            if ( phys2 == null || phys2.length != 1  ) {
+            if ( ( phys2 == null ) || ( phys2.length != 1 ) ) {
                 return false;
-                
             }
             if ( !phys2[ 0 ].toNewHampshire().equals( "((a,b),c);" ) ) {
-                System.out.println(phys2[ 0 ].toNewHampshire() );
+                System.out.println( phys2[ 0 ].toNewHampshire() );
                 return false;
             }
         }
-        catch ( Exception e ) {
+        catch ( final Exception e ) {
             e.printStackTrace();
         }
         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
                 + "]" );
@@ -1238,8 +1230,6 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        
-       
         System.out.print( "NHX parsing from URL: " );
         if ( Test.testNHXparsingFromURL() ) {
             System.out.println( "OK." );
@@ -1249,7 +1239,6 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        
         System.out.println();
         final Runtime rt = java.lang.Runtime.getRuntime();
         final long free_memory = rt.freeMemory() / 1000000;
@@ -4802,14 +4791,15 @@ public final class Test {
     private static boolean testGetLCA2() {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
+            // final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
+            final Phylogeny p_a = NHXParser.parse( "(a)" )[ 0 ];
             PhylogenyMethods.preOrderReId( p_a );
             final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
                                                                                               p_a.getNode( "a" ) );
             if ( !p_a_1.getName().equals( "a" ) ) {
                 return false;
             }
-            final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
+            final Phylogeny p_b = NHXParser.parse( "((a)b)" )[ 0 ];
             PhylogenyMethods.preOrderReId( p_b );
             final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
                                                                                               p_b.getNode( "a" ) );
@@ -7868,6 +7858,67 @@ public final class Test {
             if ( p.next() != null ) {
                 return false;
             }
+            //
+            final String p30_str = "(A,B);(C,D)";
+            final NHXParser p30 = new NHXParser();
+            p30.setSource( p30_str );
+            if ( !p30.hasNext() ) {
+                return false;
+            }
+            Phylogeny phy30 = p30.next();
+            if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
+                System.out.println( phy30.toNewHampshire() );
+                return false;
+            }
+            if ( !p30.hasNext() ) {
+                return false;
+            }
+            Phylogeny phy301 = p30.next();
+            if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
+                System.out.println( phy301.toNewHampshire() );
+                return false;
+            }
+            if ( p30.hasNext() ) {
+                return false;
+            }
+            if ( p30.hasNext() ) {
+                return false;
+            }
+            if ( p30.next() != null ) {
+                return false;
+            }
+            if ( p30.next() != null ) {
+                return false;
+            }
+            p30.reset();
+            if ( !p30.hasNext() ) {
+                return false;
+            }
+            phy30 = p30.next();
+            if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
+                System.out.println( phy30.toNewHampshire() );
+                return false;
+            }
+            if ( !p30.hasNext() ) {
+                return false;
+            }
+            phy301 = p30.next();
+            if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
+                System.out.println( phy301.toNewHampshire() );
+                return false;
+            }
+            if ( p30.hasNext() ) {
+                return false;
+            }
+            if ( p30.hasNext() ) {
+                return false;
+            }
+            if ( p30.next() != null ) {
+                return false;
+            }
+            if ( p30.next() != null ) {
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );