X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=8e402494cd59214311f49155a885dca31bbbd9b6;hb=0b49b8e750b34d28a5989facdd8a7959870de996;hp=997e52aedc9d4d521e4b423fd10dfde01c5a4381;hpb=0c6757717df4ae39a92fcea587461481dc2cde1d;p=jalview.git

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 997e52a..8e40249 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -40,6 +40,9 @@ import java.util.Locale;
 import java.util.Set;
 import java.util.SortedSet;
 
+import javax.net.ssl.HttpsURLConnection;
+import javax.net.ssl.SSLContext;
+
 import org.forester.application.support_transfer;
 import org.forester.archaeopteryx.AptxUtil;
 import org.forester.archaeopteryx.TreePanelUtil;
@@ -125,10 +128,7 @@ import org.forester.util.SequenceAccessionTools;
 import org.forester.ws.seqdb.SequenceDatabaseEntry;
 import org.forester.ws.seqdb.SequenceDbWsTools;
 import org.forester.ws.seqdb.UniProtTaxonomy;
-import org.forester.ws.wabi.TxSearch;
-import org.forester.ws.wabi.TxSearch.RANKS;
-import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
-import org.forester.ws.wabi.TxSearch.TAX_RANK;
+
 
 @SuppressWarnings( "unused")
 public final class Test {
@@ -150,7 +150,7 @@ public final class Test {
     private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
     private final static double  ZERO_DIFF                 = 1.0E-9;
 
-    public static boolean isEqual( final double a, final double b ) {
+    private static boolean isEqual( final double a, final double b ) {
         return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
     }
 
@@ -181,6 +181,7 @@ public final class Test {
             System.exit( -1 );
         }
         final long start_time = new Date().getTime();
+        
         System.out.print( "Basic node methods: " );
         if ( Test.testBasicNodeMethods() ) {
             System.out.println( "OK." );
@@ -343,6 +344,15 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
+        System.out.print( "Node construction and parsing of NHX (node level): " );
+        if ( Test.testNHXNodeParsing2() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
         System.out.print( "NHX parsing iterating: " );
         if ( Test.testNHParsingIter() ) {
             System.out.println( "OK." );
@@ -361,6 +371,15 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
+        System.out.print( "NH parsing - special chars: " );
+        if ( Test.testNHParsingSpecialChars() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
         System.out.print( "Conversion to NHX (node level): " );
         if ( Test.testNHXconversion() ) {
             System.out.println( "OK." );
@@ -487,6 +506,15 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
+        System.out.print( "UTF-8 parsing from file: " );
+        if ( Test.testUTF8ParsingFromFile() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
         System.out.print( "Copying of node data: " );
         if ( Test.testCopyOfNodeData() ) {
             System.out.println( "OK." );
@@ -971,8 +999,8 @@ public final class Test {
             }
         }
         if ( PERFORM_WEB_TREE_ACCESS ) {
-            System.out.print( "NHX parsing from URL: " );
-            if ( Test.testNHXparsingFromURL() ) {
+            System.out.print( "TreeBase acccess: " );
+            if ( Test.testTreeBaseReading() ) {
                 System.out.println( "OK." );
                 succeeded++;
             }
@@ -980,8 +1008,8 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            System.out.print( "NHX parsing from URL 2: " );
-            if ( Test.testNHXparsingFromURL2() ) {
+            System.out.print( "ToL access: " );
+            if ( Test.testToLReading() ) {
                 System.out.println( "OK." );
                 succeeded++;
             }
@@ -989,8 +1017,8 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            System.out.print( "phyloXML parsing from URL: " );
-            if ( Test.testPhyloXMLparsingFromURL() ) {
+            System.out.print( "NHX parsing from URL: " );
+            if ( Test.testNHXparsingFromURL() ) {
                 System.out.println( "OK." );
                 succeeded++;
             }
@@ -998,8 +1026,8 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            System.out.print( "TreeBase acccess: " );
-            if ( Test.testTreeBaseReading() ) {
+            System.out.print( "NHX parsing from URL 2: " );
+            if ( Test.testNHXparsingFromURL2() ) {
                 System.out.println( "OK." );
                 succeeded++;
             }
@@ -1007,9 +1035,8 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            //
-            System.out.print( "ToL access: " );
-            if ( Test.testToLReading() ) {
+            System.out.print( "phyloXML parsing from URL: " );
+            if ( Test.testPhyloXMLparsingFromURL() ) {
                 System.out.println( "OK." );
                 succeeded++;
             }
@@ -1017,7 +1044,6 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            //
             System.out.print( "TreeFam access: " );
             if ( Test.testTreeFamReading() ) {
                 System.out.println( "OK." );
@@ -1027,8 +1053,6 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            //
-            //
             System.out.print( "Pfam tree access: " );
             if ( Test.testPfamTreeReading() ) {
                 System.out.println( "OK." );
@@ -1057,7 +1081,7 @@ public final class Test {
         }
     }
 
-    public static boolean testEngulfingOverlapRemoval() {
+    private static boolean testEngulfingOverlapRemoval() {
         try {
             final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
             final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
@@ -1156,7 +1180,7 @@ public final class Test {
         return true;
     }
 
-    public static final boolean testNHXparsingFromURL2() {
+    private static final boolean testNHXparsingFromURL2() {
         try {
             final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
             final Phylogeny phys[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
@@ -1223,7 +1247,7 @@ public final class Test {
         return true;
     }
 
-    public static final boolean testNHXparsingFromURL() {
+    private static final boolean testNHXparsingFromURL() {
         try {
             final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
             final URL u = new URL( s );
@@ -1291,7 +1315,7 @@ public final class Test {
         return true;
     }
 
-    public static boolean testOverlapRemoval() {
+    private static boolean testOverlapRemoval() {
         try {
             final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
             final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
@@ -1445,15 +1469,14 @@ public final class Test {
         return true;
     }
 
-    public static final boolean testPfamTreeReading() {
+    private static final boolean testPfamTreeReading() {
         try {
             final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" );
             final NHXParser parser = new NHXParser();
             parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             parser.setReplaceUnderscores( false );
             parser.setGuessRootedness( true );
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] phys = factory.create( u.openStream(), parser );
+            final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser);
             if ( ( phys == null ) || ( phys.length != 1 ) ) {
                 return false;
             }
@@ -1463,31 +1486,37 @@ public final class Test {
         }
         catch ( final Exception e ) {
             e.printStackTrace();
+            return false;
         }
         return true;
     }
 
-    public static final boolean testPhyloXMLparsingFromURL() {
+    private static final boolean testPhyloXMLparsingFromURL() {
         try {
             final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
             final URL u = new URL( s );
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
+            final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() );
+            
             if ( ( phys == null ) || ( phys.length != 2 ) ) {
                 return false;
             }
+            final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() );
+            
+            if ( ( phys2 == null ) || ( phys2.length != 2 ) ) {
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace();
+            return false;
         }
         return true;
     }
 
-    public static final boolean testToLReading() {
+    private static final boolean testToLReading() {
         try {
             final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" );
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() );
+            final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, new TolParser() );
             if ( ( phys == null ) || ( phys.length != 1 ) ) {
                 return false;
             }
@@ -1500,47 +1529,138 @@ public final class Test {
             if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) {
                 return false;
             }
+            //
+            final URL u2 = new URL( WebserviceUtil.TOL_URL_BASE + "17706" );
+            final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, new TolParser() );
+            if ( ( phys2 == null ) || ( phys2.length != 1 ) ) {
+                return false;
+            }
+            if ( !phys2[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "17706" ) ) {
+                return false;
+            }
+            if ( phys2[ 0 ].getNumberOfExternalNodes() < 5 ) {
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace();
+            return false;
         }
         return true;
     }
 
-    public static final boolean testTreeBaseReading() {
+    private static final boolean testTreeBaseReading() {
         try {
-            final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );
+            final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "72557?format=nexus" );  
             final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
             parser.setReplaceUnderscores( true );
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] phys = factory.create( u.openStream(), parser );
+            final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser );
             if ( ( phys == null ) || ( phys.length != 1 ) ) {
                 return false;
             }
+            final URL u_1 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2406?format=nexus" );  
+            final NexusPhylogeniesParser parser_1 = new NexusPhylogeniesParser();
+            final Phylogeny[] phys_1 = ForesterUtil.readPhylogeniesFromUrl( u_1, parser_1 );
+            if ( ( phys_1 == null ) || ( phys_1.length != 1 ) ) {
+                return false;
+            }
+            final URL u_2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "422?format=nexus" );  
+            final NexusPhylogeniesParser parser_2 = new NexusPhylogeniesParser();
+            final Phylogeny[] phys_2 = ForesterUtil.readPhylogeniesFromUrl( u_2, parser_2 );
+            if ( ( phys_2 == null ) || ( phys_2.length != 1 ) ) {
+                return false;
+            }
+            final URL u_3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2654?format=nexus" );  
+            final NexusPhylogeniesParser parser_3 = new NexusPhylogeniesParser();
+            final Phylogeny[] phys_3 = ForesterUtil.readPhylogeniesFromUrl( u_3, parser_3 );
+             if ( ( phys_3 == null ) || ( phys_3.length != 1 ) ) {
+                return false;
+            }
+            final URL u_4 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );  
+            final NexusPhylogeniesParser parser_4 = new NexusPhylogeniesParser();
+            final Phylogeny[] phys_4 = ForesterUtil.readPhylogeniesFromUrl( u_4, parser_4 );
+             if ( ( phys_4 == null ) || ( phys_4.length != 1 ) ) {
+                return false;
+            }
             final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" );
             final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser();
             parser2.setReplaceUnderscores( true );
-            final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 );
+            final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, parser2 );
             if ( ( phys2 == null ) || ( phys2.length != 9 ) ) {
                 return false;
             }
+            final URL u3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14909?format=nexus" );
+            final NexusPhylogeniesParser parser3 = new NexusPhylogeniesParser();
+            final Phylogeny[] phys3 = ForesterUtil.readPhylogeniesFromUrl( u3, parser3 );
+            if ( ( phys3 == null ) || ( phys3.length != 2 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys4 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14525?format=nexus" ),
+                    new NexusPhylogeniesParser() );
+            if ( ( phys4 == null ) || ( phys4.length != 1 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys5 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15632?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys5 == null ) || ( phys5.length != 1 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys6 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "10190?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys6 == null ) || ( phys6.length != 1 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys7 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "13246?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys7 == null ) || ( phys7.length != 2 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys8 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "11662?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys8 == null ) || ( phys8.length != 2 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys9 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "562?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys9 == null ) || ( phys9.length != 4 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys16424 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "16424?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys16424 == null ) || ( phys16424.length != 1 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys17878 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "17878?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys17878 == null ) || ( phys17878.length != 17 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys18804 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "18804?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys18804 == null ) || ( phys18804.length != 2 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys346 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "346?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys346 == null ) || ( phys346.length != 1 ) ) {
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace();
+            return false;
         }
         return true;
     }
 
-    public static final boolean testTreeFamReading() {
+    private static final boolean testTreeFamReading() {
         try {
             final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" );
             final NHXParser parser = new NHXParser();
             parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
             parser.setReplaceUnderscores( false );
             parser.setGuessRootedness( true );
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] phys = factory.create( u.openStream(), parser );
+            final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser );
             if ( ( phys == null ) || ( phys.length != 1 ) ) {
                 return false;
             }
@@ -1550,6 +1670,7 @@ public final class Test {
         }
         catch ( final Exception e ) {
             e.printStackTrace();
+            return false;
         }
         return true;
     }
@@ -1696,12 +1817,258 @@ public final class Test {
         }
         return true;
     }
+    
+    private static boolean testUTF8ParsingFromFile() {
+        try {
+            final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
+            final Phylogeny[] phylogenies_xml = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.xml" ),
+                                                              xml_parser );
+            if ( xml_parser.getErrorCount() > 0 ) {
+                System.out.println( xml_parser.getErrorMessages().toString() );
+                return false;
+            }
+            if ( phylogenies_xml.length != 1 ) {
+                return false;
+            }
+         
+            final Phylogeny[] phylogenies_xml2 = ParserBasedPhylogenyFactory.getInstance().create( new StringBuffer( phylogenies_xml[0].toPhyloXML( 0 )),
+                                                                                                   xml_parser );
+            
+            final Phylogeny[] phylogenies_nh = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.nh" ), new NHXParser() );
+            if ( phylogenies_nh.length != 1 ) {
+                return false;
+            }
+           
+            final Phylogeny[] phylogenies_nex = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.nex" ), new NexusPhylogeniesParser() );
+            if ( phylogenies_nex.length != 1 ) {
+                return false;
+            }
+          
+            final String[] xml_n = phylogenies_xml[0].getAllExternalNodeNames();
+            final String[] xml_n2 = phylogenies_xml2[0].getAllExternalNodeNames();
+            final String[] nh_n = phylogenies_nh[0].getAllExternalNodeNames();
+            final String[] nex_n = phylogenies_nex[0].getAllExternalNodeNames();
+            final String n0 = "AQ~!@#$%^&*()_+-=\\{}|;:\"<>?,./";
+            final String n1 = "€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ";
+            final String n2 = "漢字ひらがなカタカナ";
+            final String n3 = "อักษรไทย";
+            final String n4 = "繁體字";
+            final String n5 = "한글";
+            final String n6 = "देवनागरी";
+            
+            final String n7 = "chữ Quốc ngữ";
+            final String n8 = "ру́сский язы́к";
+            final String n9 = "អក្សរខ្មែរ";
+            
+            if ( !xml_n[0].equals( n0 ) ) {
+                System.out.println( xml_n[0] );
+                System.out.println( n0 );
+                return false;
+            }
+            if ( !xml_n2[0].equals( n0 ) ) {
+                System.out.println( xml_n2[0] );
+                System.out.println( n0 );
+                return false;
+            }
+            if ( !nh_n[0].equals( n0 ) ) {
+                System.out.println( nh_n[0] );
+                System.out.println( n0 );
+                return false;
+            }
+            if ( !nex_n[0].equals( n0 ) ) {
+                System.out.println( nex_n[0] );
+                System.out.println( n0 );
+                return false;
+            }
+            
+            if ( !xml_n[1].equals( n1 ) ) {
+                System.out.println( xml_n[1] );
+                System.out.println( n1 );
+                return false;
+            }
+            if ( !xml_n2[1].equals( n1 ) ) {
+                System.out.println( xml_n2[1] );
+                System.out.println( n1 );
+                return false;
+            }
+            if ( !nh_n[1].equals( n1 ) ) {
+                System.out.println( nh_n[1] );
+                System.out.println( n1 );
+                return false;
+            }
+            if ( !nex_n[1].equals( n1 ) ) {
+                System.out.println( nex_n[1] );
+                System.out.println( n1 );
+                return false;
+            }
+            
+            if ( !xml_n[2].equals( n2 ) ) {
+                System.out.println( xml_n[2] );
+                System.out.println( n2 );
+                return false;
+            }
+            if ( !xml_n2[2].equals( n2 ) ) {
+                System.out.println( xml_n2[2] );
+                System.out.println( n2 );
+                return false;
+            }
+            if ( !nh_n[2].equals( n2 ) ) {
+                System.out.println( nh_n[2] );
+                System.out.println( n2 );
+                return false;
+            }
+            if ( !nex_n[2].equals( n2 ) ) {
+                System.out.println( nex_n[2] );
+                System.out.println( n2 );
+                return false;
+            }
+            //
+            if ( !xml_n[3].equals( n3 ) ) {
+                System.out.println( xml_n[3] );
+                System.out.println( n3 );
+                return false;
+            }
+            if ( !xml_n2[3].equals( n3 ) ) {
+                System.out.println( xml_n2[3] );
+                System.out.println( n3 );
+                return false;
+            }
+            if ( !nh_n[3].equals( n3 ) ) {
+                System.out.println( nh_n[3] );
+                System.out.println( n3 );
+                return false;
+            }
+            if ( !nex_n[3].equals( n3 ) ) {
+                System.out.println( nex_n[3] );
+                System.out.println( n3 );
+                return false;
+            }
+            //
+            if ( !xml_n[4].equals( n4 ) ) {
+                System.out.println( xml_n[4] );
+                System.out.println( n4 );
+                return false;
+            }
+            if ( !nh_n[4].equals( n4 ) ) {
+                System.out.println( nh_n[4] );
+                System.out.println( n4 );
+                return false;
+            }
+            if ( !nex_n[4].equals( n4 ) ) {
+                System.out.println( nex_n[4] );
+                System.out.println( n4 );
+                return false;
+            }
+            //
+            if ( !xml_n[5].equals( n5 ) ) {
+                System.out.println( xml_n[5] );
+                System.out.println( n5 );
+                return false;
+            }
+            if ( !nh_n[5].equals( n5 ) ) {
+                System.out.println( nh_n[5] );
+                System.out.println( n5 );
+                return false;
+            }
+            if ( !nex_n[5].equals( n5 ) ) {
+                System.out.println( nex_n[5] );
+                System.out.println( n5 );
+                return false;
+            }
+            //
+            if ( !xml_n[6].equals( n6 ) ) {
+                System.out.println( xml_n[6] );
+                System.out.println( n6 );
+                return false;
+            }
+            if ( !nh_n[6].equals( n6 ) ) {
+                System.out.println( nh_n[6] );
+                System.out.println( n6 );
+                return false;
+            }
+            if ( !nex_n[6].equals( n6 ) ) {
+                System.out.println( nex_n[6] );
+                System.out.println( n6 );
+                return false;
+            }
+            //
+            if ( !xml_n[7].equals( n7 ) ) {
+                System.out.println( xml_n[7] );
+                System.out.println( n7 );
+                return false;
+            }
+            if ( !nh_n[7].equals( n7 ) ) {
+                System.out.println( nh_n[7] );
+                System.out.println( n7 );
+                return false;
+            }
+            if ( !nex_n[7].equals( n7 ) ) {
+                System.out.println( nex_n[7] );
+                System.out.println( n7 );
+                return false;
+            }
+            if ( !xml_n[8].equals( n8 ) ) {
+                System.out.println( xml_n[8] );
+                System.out.println( n8 );
+                return false;
+            }
+            if ( !nh_n[8].equals( n8 ) ) {
+                System.out.println( nh_n[8] );
+                System.out.println( n8 );
+                return false;
+            }
+            if ( !nex_n[8].equals( n8 ) ) {
+                System.out.println( nex_n[8] );
+                System.out.println( n8 );
+                return false;
+            }
+            if ( !xml_n[9].equals( n9 ) ) {
+                System.out.println( xml_n[9] );
+                System.out.println( n9 );
+                return false;
+            }
+            if ( !xml_n2[9].equals( n9 ) ) {
+                System.out.println( xml_n2[9] );
+                System.out.println( n9 );
+                return false;
+            }
+            if ( !nh_n[9].equals( n9 ) ) {
+                System.out.println( nh_n[9] );
+                System.out.println( n9 );
+                return false;
+            }
+            if ( !nex_n[9].equals( n9 ) ) {
+                System.out.println( nex_n[9] );
+                System.out.println( n9 );
+                return false;
+            }
+            if (!phylogenies_xml[0].toNewHampshire().equals( 
+                                                            phylogenies_nh[0].toNewHampshire() ) ) {
+                System.out.println( phylogenies_xml[0].toNewHampshire() );
+                System.out.println( phylogenies_nh[0].toNewHampshire() );
+                return false;
+            }
+            if (!phylogenies_xml[0].toNewHampshire().equals( 
+                                                            phylogenies_nex[0].toNewHampshire() ) ) {
+                System.out.println( phylogenies_xml[0].toNewHampshire() );
+                System.out.println( phylogenies_nex[0].toNewHampshire() );
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
+    
 
     private static boolean testBasicPhyloXMLparsing() {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
-            final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
+            final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ),
                                                               xml_parser );
             if ( xml_parser.getErrorCount() > 0 ) {
                 System.out.println( xml_parser.getErrorMessages().toString() );
@@ -1915,7 +2282,7 @@ public final class Test {
             else {
                 xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
             }
-            final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
+            final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ),
                                                               xml_parser );
             if ( xml_parser.getErrorCount() > 0 ) {
                 System.out.println( xml_parser.getErrorMessages().toString() );
@@ -2081,6 +2448,7 @@ public final class Test {
             }
             if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
                     .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
+                System.out.println( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() );
                 return false;
             }
             if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
@@ -2267,7 +2635,7 @@ public final class Test {
                     xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
                 }
             }
-            final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
+            final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ),
                                                               xml_parser );
             if ( xml_parser.getErrorCount() > 0 ) {
                 System.out.println( xml_parser.getErrorMessages().toString() );
@@ -2302,7 +2670,7 @@ public final class Test {
                 return false;
             }
             final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
-            final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
+            final Phylogeny[] phylogenies_1 = factory.create( new File( x2 ), xml_parser );
             if ( xml_parser.getErrorCount() > 0 ) {
                 System.out.println( "errors:" );
                 System.out.println( xml_parser.getErrorMessages().toString() );
@@ -2311,7 +2679,7 @@ public final class Test {
             if ( phylogenies_1.length != 4 ) {
                 return false;
             }
-            final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
+            final Phylogeny[] phylogenies_2 = factory.create( new File(Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml" ),
                                                               xml_parser );
             if ( xml_parser.getErrorCount() > 0 ) {
                 System.out.println( "errors:" );
@@ -2324,7 +2692,7 @@ public final class Test {
             if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
                 return false;
             }
-            final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
+            final Phylogeny[] phylogenies_3 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml" ),
                                                               xml_parser );
             if ( xml_parser.getErrorCount() > 0 ) {
                 System.out.println( xml_parser.getErrorMessages().toString() );
@@ -2346,7 +2714,7 @@ public final class Test {
             if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
                 return false;
             }
-            final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
+            final Phylogeny[] phylogenies_4 = factory.create( new File( Test.PATH_TO_TEST_DATA + "special_characters.xml") ,
                                                               xml_parser );
             if ( xml_parser.getErrorCount() > 0 ) {
                 System.out.println( xml_parser.getErrorMessages().toString() );
@@ -2970,7 +3338,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
-            final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
+            final Phylogeny t5 = factory.create( sb5.toString(), new NHXParser() )[ 0 ];
             if ( t5.getNumberOfExternalNodes() != 8 ) {
                 return false;
             }
@@ -2978,17 +3346,17 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
-            final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
+            final Phylogeny t6 = factory.create( sb6.toString(), new NHXParser() )[ 0 ];
             if ( t6.getHeight() != 15 ) {
                 return false;
             }
             final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" );
-            final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
+            final Phylogeny t7 = factory.create( sb7.toString(), new NHXParser() )[ 0 ];
             if ( t7.getHeight() != 15 ) {
                 return false;
             }
             final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" );
-            final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
+            final Phylogeny t8 = factory.create( sb8.toString(), new NHXParser() )[ 0 ];
             if ( t8.getNumberOfExternalNodes() != 10 ) {
                 return false;
             }
@@ -4894,12 +5262,22 @@ public final class Test {
 
     private static boolean testFastaParser() {
         try {
-            if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
+            FileInputStream fis1 = new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" );
+            if ( !FastaParser.isLikelyFasta( fis1 ) ) {
+                fis1.close();
                 return false;
             }
-            if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
+            else {
+                fis1.close();
+            }
+            FileInputStream fis2 = new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" );
+            if ( FastaParser.isLikelyFasta( fis2 ) ) {
+                fis2.close();
                 return false;
             }
+            else {
+                fis2.close();
+            }
             final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
             if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
                 return false;
@@ -6466,7 +6844,7 @@ public final class Test {
             PhylogenyNode n;
             List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
             final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
-            final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
+            final Phylogeny t0 = factory.create( sb0.toString(), new NHXParser() )[ 0 ];
             t0.getNode( "cd" ).setCollapse( true );
             t0.getNode( "cde" ).setCollapse( true );
             n = t0.getFirstExternalNode();
@@ -6494,7 +6872,7 @@ public final class Test {
             }
             ext.clear();
             final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
-            final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
+            final Phylogeny t1 = factory.create( sb1.toString(), new NHXParser() )[ 0 ];
             t1.getNode( "ab" ).setCollapse( true );
             t1.getNode( "cd" ).setCollapse( true );
             t1.getNode( "cde" ).setCollapse( true );
@@ -6521,7 +6899,7 @@ public final class Test {
             }
             ext.clear();
             final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
+            final Phylogeny t2 = factory.create( sb2.toString(), new NHXParser() )[ 0 ];
             t2.getNode( "ab" ).setCollapse( true );
             t2.getNode( "cd" ).setCollapse( true );
             t2.getNode( "cde" ).setCollapse( true );
@@ -6549,7 +6927,7 @@ public final class Test {
             }
             ext.clear();
             final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
+            final Phylogeny t3 = factory.create( sb3.toString(), new NHXParser() )[ 0 ];
             t3.getNode( "ab" ).setCollapse( true );
             t3.getNode( "cd" ).setCollapse( true );
             t3.getNode( "cde" ).setCollapse( true );
@@ -6575,7 +6953,7 @@ public final class Test {
             }
             ext.clear();
             final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
+            final Phylogeny t4 = factory.create( sb4.toString(), new NHXParser() )[ 0 ];
             t4.getNode( "ab" ).setCollapse( true );
             t4.getNode( "cd" ).setCollapse( true );
             t4.getNode( "cde" ).setCollapse( true );
@@ -6590,7 +6968,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
-            final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
+            final Phylogeny t5 = factory.create( sb5.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             n = t5.getFirstExternalNode();
             while ( n != null ) {
@@ -6625,7 +7003,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
-            final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
+            final Phylogeny t6 = factory.create( sb6.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             t6.getNode( "ab" ).setCollapse( true );
             n = t6.getNode( "ab" );
@@ -6658,7 +7036,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
-            final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
+            final Phylogeny t7 = factory.create( sb7.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             t7.getNode( "cd" ).setCollapse( true );
             n = t7.getNode( "a" );
@@ -6691,7 +7069,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
-            final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
+            final Phylogeny t8 = factory.create( sb8.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             t8.getNode( "cd" ).setCollapse( true );
             t8.getNode( "c" ).setCollapse( true );
@@ -6727,7 +7105,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
+            final Phylogeny t9 = factory.create( sb9.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             t9.getNode( "gh" ).setCollapse( true );
             n = t9.getNode( "a" );
@@ -6760,7 +7138,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
+            final Phylogeny t10 = factory.create( sb10.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             t10.getNode( "gh" ).setCollapse( true );
             t10.getNode( "g" ).setCollapse( true );
@@ -6795,7 +7173,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
+            final Phylogeny t11 = factory.create( sb11.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             t11.getNode( "gh" ).setCollapse( true );
             t11.getNode( "fgh" ).setCollapse( true );
@@ -6826,7 +7204,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
+            final Phylogeny t12 = factory.create( sb12.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             t12.getNode( "gh" ).setCollapse( true );
             t12.getNode( "fgh" ).setCollapse( true );
@@ -6860,7 +7238,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
+            final Phylogeny t13 = factory.create( sb13.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             t13.getNode( "ab" ).setCollapse( true );
             t13.getNode( "b" ).setCollapse( true );
@@ -6890,7 +7268,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
+            final Phylogeny t14 = factory.create( sb14.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             t14.getNode( "ab" ).setCollapse( true );
             t14.getNode( "a" ).setCollapse( true );
@@ -6920,7 +7298,7 @@ public final class Test {
                 return false;
             }
             final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
+            final Phylogeny t15 = factory.create( sb15.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             t15.getNode( "ab" ).setCollapse( true );
             t15.getNode( "a" ).setCollapse( true );
@@ -6955,7 +7333,7 @@ public final class Test {
             //
             //
             final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
+            final Phylogeny t16 = factory.create( sb16.toString(), new NHXParser() )[ 0 ];
             ext.clear();
             t16.getNode( "ab" ).setCollapse( true );
             t16.getNode( "a" ).setCollapse( true );
@@ -8175,10 +8553,10 @@ public final class Test {
             if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
                 return false;
             }
-            final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
+            final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ).toString(), new NHXParser() )[ 0 ];
             final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
             final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
-            final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
+            final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ).toString(), new NHXParser() )[ 0 ];
             final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
             final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
             final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
@@ -8436,21 +8814,21 @@ public final class Test {
             if ( p46.length != 0 ) {
                 return false;
             }
-            final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
+            final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ).toString(), new NHXParser() )[ 0 ];
             if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
                 return false;
             }
-            final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+            final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ];
             if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
                 return false;
             }
             final Phylogeny p49 = factory
-                    .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
+                    .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ).toString(),
                              new NHXParser() )[ 0 ];
             if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
                 return false;
             }
-            final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+            final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ];
             if ( p50.getNode( "A" ) == null ) {
                 return false;
             }
@@ -8465,21 +8843,21 @@ public final class Test {
                     .equals( "((A,B)88:2.0,C);" ) ) {
                 return false;
             }
-            final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+            final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ];
             if ( p51.getNode( "A(A" ) == null ) {
                 return false;
             }
-            final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+            final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ];
             if ( p52.getNode( "A(A" ) == null ) {
                 return false;
             }
             final Phylogeny p53 = factory
-                    .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
+                    .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ).toString(),
                              new NHXParser() )[ 0 ];
             if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
                 return false;
             }
-            final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
+            final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ).toString(), new NHXParser() )[ 0 ];
             if ( p54.getNode( "A" ) == null ) {
                 return false;
             }
@@ -8487,7 +8865,7 @@ public final class Test {
                 return false;
             }
             final Phylogeny p55 = factory
-                    .create( new StringBuffer( "((\"lcl|HPV32_L1.:1  s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ),
+                    .create( new StringBuffer( "((\"lcl|HPV32_L1.:1  s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ).toString(),
                              new NHXParser() )[ 0 ];
             if ( !p55
                     .toNewHampshire()
@@ -8496,7 +8874,7 @@ public final class Test {
                 return false;
             }
             final Phylogeny p56 = factory
-                    .create( new StringBuffer( "((\"lcl|HPV32_L1.:1      s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
+                    .create( new StringBuffer( "((\"lcl|HPV32_L1.:1      s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ).toString(),
                              new NHXParser() )[ 0 ];
             if ( !p56
                     .toNewHampshire()
@@ -8505,7 +8883,7 @@ public final class Test {
                 return false;
             }
             final Phylogeny p57 = factory
-                    .create( new StringBuffer( "((\"lcl|HPV32_L1.:1      s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
+                    .create( new StringBuffer( "((\"lcl|HPV32_L1.:1      s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ).toString(),
                              new NHXParser() )[ 0 ];
             if ( !p57
                     .toNewHampshire()
@@ -8514,30 +8892,58 @@ public final class Test {
                 return false;
             }
             final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';";
-            final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ];
+            final Phylogeny p58 = factory.create( s58, new NHXParser() )[ 0 ];
             if ( !p58.toNewHampshire().equals( s58 ) ) {
                 System.out.println( p58.toNewHampshire() );
                 return false;
             }
             final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";";
-            final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ];
+            final Phylogeny p59 = factory.create( s59 , new NHXParser() )[ 0 ];
             if ( !p59.toNewHampshire().equals( s59 ) ) {
                 System.out.println( p59.toNewHampshire() );
                 return false;
             }
             final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');";
-            final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ];
+            final Phylogeny p60 = factory.create( s60, new NHXParser() )[ 0 ];
             if ( !p60.toNewHampshire().equals( s60 ) ) {
                 System.out.println( p60.toNewHampshire() );
                 return false;
             }
             final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';";
-            final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ];
+            final Phylogeny p61 = factory.create( s61, new NHXParser() )[ 0 ];
             if ( !p61.toNewHampshire()
                     .equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) {
                 System.out.println( p61.toNewHampshire() );
                 return false;
             }
+            final String s62 = "(1[&type=\"X\",size=123,subtree=(1,2);]:0.003,2[&type=\"(X,Y:3)\"]:0.004)[&type=\"(X,Y)\"]:0.0;";
+            final Phylogeny p62 = factory.create( s62, new NHXParser() )[ 0 ];
+            if ( !p62.toNewHampshire()
+                    .equals( "(1:0.003,2:0.004):0.0;" ) ) {
+                System.out.println( p62.toNewHampshire() );
+                return false;
+            }
+            final String s63 = "(1:0.003[&type=\"X\",size=123,subtree=(1,2);],2:0.004[&type=\"(X,Y:3)\"]):0.0[&type=\"(X,Y)\"];";
+            final Phylogeny p63 = factory.create( s63, new NHXParser() )[ 0 ];
+            if ( !p63.toNewHampshire()
+                    .equals( "(1:0.003,2:0.004):0.0;" ) ) {
+                System.out.println( p63.toNewHampshire() );
+                return false;
+            }
+            final String s64 = "((1,2):[95.5],3);";
+            final Phylogeny p64 = factory.create( s64, new NHXParser() )[ 0 ];
+            if ( !p64.toNewHampshireX()
+                    .equals( "((1,2)[&&NHX:B=95.5],3)" ) ) {
+                System.out.println( p64.toNewHampshireX() );
+                return false;
+            }
+            final String s65 = "((1:0.1,2:0.2):0.3[10.2],3);";
+            final Phylogeny p65 = factory.create( s65, new NHXParser() )[ 0 ];
+            if ( !p65.toNewHampshireX()
+                    .equals( "((1:0.1,2:0.2):0.3[&&NHX:B=10.2],3)" ) ) {
+                System.out.println( p65.toNewHampshireX() );
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );
@@ -8545,7 +8951,36 @@ public final class Test {
         }
         return true;
     }
-
+    
+    private static boolean testNHParsingSpecialChars() {
+        try {
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();   
+            final String i0 = "(A!+=~QWERTY!@#$%^&*-,€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ)";
+            final Phylogeny p0 = factory.create( i0, new NHXParser() )[ 0 ];
+            if ( !p0.toNewHampshireX().equals( i0 ) ) {
+                System.out.println();
+                System.out.println( p0.toNewHampshireX() );
+                System.out.println( i0 );
+                return false;
+            }
+            final String i1 = "(हिंदी,한글,ไทย,'Tiếng Việt',ひらがなカタカナ漢字,繁體字,русский)";
+            final Phylogeny p1 = factory.create( i1, new NHXParser() )[ 0 ];
+            if ( !p1.toNewHampshireX().equals( i1 ) ) {
+                System.out.println();
+                System.out.println( p1.toNewHampshireX() );
+                System.out.println( i1 );
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
+    
+    
     private static boolean testNHParsingIter() {
         try {
             final String p0_str = "(A,B);";
@@ -9407,6 +9842,151 @@ public final class Test {
         return true;
     }
 
+    
+    private static boolean testNHXNodeParsing2() {
+        try {
+          
+            final PhylogenyNode n0_0 = PhylogenyNode
+                    .createInstanceFromNhxString( "n0:[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n0_0.getName().equals( "n0" ) ) {
+                return false;
+            }
+            if ( !isEqual( n0_0.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n0_1 = PhylogenyNode
+                    .createInstanceFromNhxString( "n0[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n0_1.getName().equals( "n0" ) ) {
+                return false;
+            }
+            if ( !isEqual( n0_1.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n0_2 = PhylogenyNode
+                    .createInstanceFromNhxString( "n0:1E-3[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n0_2.getName().equals( "n0" ) ) {
+                return false;
+            }
+            if ( !isEqual( n0_2.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n0_3 = PhylogenyNode
+                    .createInstanceFromNhxString( "n0:1E-3:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n0_3.getName().equals( "n0" ) ) {
+                return false;
+            }
+            if ( !isEqual( n0_3.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n0_4 = PhylogenyNode
+                    .createInstanceFromNhxString( "n0:0.001:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n0_4.getName().equals( "n0" ) ) {
+                return false;
+            }
+            if ( !isEqual( n0_4.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n1_0 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_0.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( n1_0.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+               return false;
+            }
+            final PhylogenyNode n1_1 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]:0.001", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_1.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( n1_1.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+               return false;
+            }
+            if ( !isEqual( n1_1.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n1_2 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:0.001[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_2.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( n1_2.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+               return false;
+            }
+            if ( !isEqual( n1_2.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n1_3 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[&boostrap=69,&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_3.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( n1_3.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+               return false;
+            }
+            if ( !isEqual( n1_3.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_3.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+                return false;
+            }
+            if ( !n1_3.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) {
+                return false;
+            }
+            final PhylogenyNode n1_4 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&bootstrap=69,&!colour=#FFFFFF]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_4.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( n1_4.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+               return false;
+            }
+            if ( !isEqual( n1_4.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_4.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+                return false;
+            }
+            if ( !n1_4.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) {
+                return false;
+            }
+            final PhylogenyNode n1_5 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[69.0]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_5.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_5.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_5.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+                return false;
+            }       
+            final PhylogenyNode n1_6 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_6.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+           
+            if ( !isEqual( n1_6.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getStandardDeviation(), 0.11 ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getValue(), 0.95 ) ) {
+                return false;
+            }
+            if ( !n1_6.getBranchData().getConfidence( 0 ).getType().equals( "posterior probability" ) ) {
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
     private static boolean testNHXParsing() {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
@@ -9729,7 +10309,7 @@ public final class Test {
                     xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
                 }
             }
-            final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
+            final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml" ),
                                                               xml_parser );
             if ( xml_parser.getErrorCount() > 0 ) {
                 System.out.println( xml_parser.getErrorMessages().toString() );
@@ -12917,60 +13497,6 @@ public final class Test {
         }
         return true;
     }
-
-    private static boolean testWabiTxSearch() {
-        try {
-            String result = "";
-            result = TxSearch.searchSimple( "nematostella" );
-            result = TxSearch.getTxId( "nematostella" );
-            if ( !result.equals( "45350" ) ) {
-                return false;
-            }
-            result = TxSearch.getTxName( "45350" );
-            if ( !result.equals( "Nematostella" ) ) {
-                return false;
-            }
-            result = TxSearch.getTxId( "nematostella vectensis" );
-            if ( !result.equals( "45351" ) ) {
-                return false;
-            }
-            result = TxSearch.getTxName( "45351" );
-            if ( !result.equals( "Nematostella vectensis" ) ) {
-                return false;
-            }
-            result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
-            if ( !result.equals( "536089" ) ) {
-                return false;
-            }
-            result = TxSearch.getTxName( "536089" );
-            if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
-                return false;
-            }
-            final List<String> queries = new ArrayList<String>();
-            queries.add( "Campylobacter coli" );
-            queries.add( "Escherichia coli" );
-            queries.add( "Arabidopsis" );
-            queries.add( "Trichoplax" );
-            queries.add( "Samanea saman" );
-            queries.add( "Kluyveromyces marxianus" );
-            queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
-            queries.add( "Bornavirus parrot/PDD/2008" );
-            final List<RANKS> ranks = new ArrayList<RANKS>();
-            ranks.add( RANKS.SUPERKINGDOM );
-            ranks.add( RANKS.KINGDOM );
-            ranks.add( RANKS.FAMILY );
-            ranks.add( RANKS.GENUS );
-            ranks.add( RANKS.TRIBE );
-            result = TxSearch.searchLineage( queries, ranks );
-            result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
-            result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
-        }
-        catch ( final Exception e ) {
-            System.out.println();
-            System.out.println( "the following might be due to absence internet connection:" );
-            e.printStackTrace( System.out );
-            return false;
-        }
-        return true;
-    }
+    
+    
 }