taxonomy code more stringent now

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 1a113ab..96febec 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -1385,7 +1385,7 @@ public final class MainFrameApplication extends MainFrame {
                     final String name = n.getName().trim();
                     if ( !ForesterUtil.isEmpty( name ) ) {
                         final String code = ParserUtils
-                                .extractTaxonomyCodeFromNodeName( name, false, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
+                                .extractTaxonomyCodeFromNodeName( name, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
                         if ( !ForesterUtil.isEmpty( code ) ) {
                             PhylogenyMethods.setTaxonomyCode( n, code );
                         }

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 f03ed69..c1cfa40 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -61,17 +61,16 @@ import org.forester.util.ForesterUtil;
 
 public final class NHXParser implements PhylogenyParser {
 
-    public static final boolean                              LIMIT_SPECIES_NAMES_TO_FIVE_CHARS = false;
-    public static final PhylogenyMethods.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION_DEFAULT       = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
-    final static private boolean                             GUESS_ROOTEDNESS_DEFAULT          = true;
-    final static private boolean                             GUESS_IF_SUPPORT_VALUES           = true;
-    final static private boolean                             IGNORE_QUOTES_DEFAULT             = false;
-    final static public boolean                              REPLACE_UNDERSCORES_DEFAULT       = false;
+    public static final PhylogenyMethods.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION_DEFAULT = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
+    final static private boolean                             GUESS_ROOTEDNESS_DEFAULT    = true;
+    final static private boolean                             GUESS_IF_SUPPORT_VALUES     = true;
+    final static private boolean                             IGNORE_QUOTES_DEFAULT       = false;
+    final static public boolean                              REPLACE_UNDERSCORES_DEFAULT = false;
     private boolean                                          _saw_closing_paren;
-    final static private byte                                STRING                            = 0;
-    final static private byte                                STRING_BUFFER                     = 1;
-    final static private byte                                CHAR_ARRAY                        = 2;
-    final static private byte                                BUFFERED_READER                   = 3;
+    final static private byte                                STRING                      = 0;
+    final static private byte                                STRING_BUFFER               = 1;
+    final static private byte                                CHAR_ARRAY                  = 2;
+    final static private byte                                BUFFERED_READER             = 3;
     private boolean                                          _guess_rootedness;
     private boolean                                          _has_next;
     private boolean                                          _ignore_quotes;
@@ -85,16 +84,16 @@ public final class NHXParser implements PhylogenyParser {
     private Phylogeny                                        _current_phylogeny;
     private PhylogenyMethods.TAXONOMY_EXTRACTION             _taxonomy_extraction;
     private boolean                                          _replace_underscores;
-    public final static Pattern                              UC_LETTERS_NUMBERS_PATTERN        = Pattern
-                                                                                                       .compile( "^[A-Z0-9]+$" );
-    public final static Pattern                              NUMBERS_ONLY_PATTERN              = Pattern
-                                                                                                       .compile( "^[0-9\\.]+$" );
-    public final static Pattern                              MB_PROB_PATTERN                   = Pattern
-                                                                                                       .compile( "prob=([^,]+)" );
-    public final static Pattern                              MB_PROB_SD_PATTERN                = Pattern
-                                                                                                       .compile( "prob_stddev=([^,]+)" );
-    public final static Pattern                              MB_BL_PATTERN                     = Pattern
-                                                                                                       .compile( "length_median=([^,]+)" );
+    public final static Pattern                              UC_LETTERS_NUMBERS_PATTERN  = Pattern
+                                                                                                 .compile( "^[A-Z0-9]+$" );
+    public final static Pattern                              NUMBERS_ONLY_PATTERN        = Pattern
+                                                                                                 .compile( "^[0-9\\.]+$" );
+    public final static Pattern                              MB_PROB_PATTERN             = Pattern
+                                                                                                 .compile( "prob=([^,]+)" );
+    public final static Pattern                              MB_PROB_SD_PATTERN          = Pattern
+                                                                                                 .compile( "prob_stddev=([^,]+)" );
+    public final static Pattern                              MB_BL_PATTERN               = Pattern
+                                                                                                 .compile( "length_median=([^,]+)" );
 
     public NHXParser() {
         init();
@@ -692,10 +691,8 @@ public final class NHXParser implements PhylogenyParser {
                     node_to_annotate.setName( t.nextToken() );
                     if ( !replace_underscores
                             && ( !is_nhx && ( taxonomy_extraction != PhylogenyMethods.TAXONOMY_EXTRACTION.NO ) ) ) {
-                        final String tax = ParserUtils
-                                .extractTaxonomyCodeFromNodeName( node_to_annotate.getName(),
-                                                                  LIMIT_SPECIES_NAMES_TO_FIVE_CHARS,
-                                                                  taxonomy_extraction );
+                        final String tax = ParserUtils.extractTaxonomyCodeFromNodeName( node_to_annotate.getName(),
+                                                                                        taxonomy_extraction );
                         if ( !ForesterUtil.isEmpty( tax ) ) {
                             if ( !node_to_annotate.getNodeData().isHasTaxonomy() ) {
                                 node_to_annotate.getNodeData().setTaxonomy( new Taxonomy() );

diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java
index 5c08974..b8de6cf 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java
@@ -193,18 +193,12 @@ public class PhyloXmlParser implements PhylogenyParser {
             else if ( getSource() instanceof InputStream ) {
                 if ( !isZippedInputstream() ) {
                     final InputStream is = ( InputStream ) getSource();
-                    final Reader reader = new InputStreamReader( is );
-                    xml_reader.parse( new InputSource( reader ) );
+                    xml_reader.parse( new InputSource( new InputStreamReader( is ) ) );
                 }
                 else {
                     final ZipInputStream zip_is = new ZipInputStream( ( InputStream ) getSource() );
                     zip_is.getNextEntry();
-                    final Reader reader = new InputStreamReader( zip_is );
-                    if ( reader == null ) {
-                        throw new PhylogenyParserException( "zip input stream \"" + getSource()
-                                + "\" appears not to contain any (phyloXML) data" );
-                    }
-                    xml_reader.parse( new InputSource( reader ) );
+                    xml_reader.parse( new InputSource( new InputStreamReader( zip_is ) ) );
                 }
             }
             else if ( getSource() instanceof String ) {

diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java
index 9ccfdf9..5083c91 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java
@@ -36,8 +36,7 @@ public final class PhyloXmlUtil {
     public static final String       OTHER                                      = "other";
     public static final String       UNKNOWN                                    = "unknown";
     public final static Pattern      SEQUENCE_SYMBOL_PATTERN                    = Pattern.compile( "\\S{1,20}" );
-    public final static Pattern      TAXOMONY_CODE_PATTERN                      = Pattern
-                                                                                        .compile( "[a-zA-Z0-9_]{1,10}" );
+    public final static Pattern      TAXOMONY_CODE_PATTERN                      = Pattern.compile( "[A-Z0-9]{3,5}" );
     public final static Pattern      LIT_REF_DOI_PATTERN                        = Pattern
                                                                                         .compile( "[a-zA-Z0-9_\\.]+\\S+" );
     public final static Set<String>  SEQUENCE_TYPES                             = new HashSet<String>();

diff --git a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
index bb89472..58a48ff 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
+++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
@@ -36,6 +36,7 @@ import java.io.InputStreamReader;
 import java.io.StringReader;
 import java.net.URL;
 import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
@@ -49,6 +50,9 @@ import org.forester.util.ForesterUtil;
 
 public final class ParserUtils {
 
+    final private static Pattern TAXOMONY_CODE_PATTERN_1 = Pattern.compile( "[A-Z0-9]{5}" );
+    final private static Pattern TAXOMONY_CODE_PATTERN_2 = Pattern.compile( "([A-Z0-9]{5})[^A-Z].*" );
+
     final public static PhylogenyParser createParserDependingFileContents( final File file,
                                                                            final boolean phyloxml_validate_against_xsd )
             throws FileNotFoundException, IOException {
@@ -218,11 +222,9 @@ public final class ParserUtils {
      * Return null if no code extractable.
      * 
      * @param name
-     * @param limit_to_five
      * @return
      */
     public static String extractTaxonomyCodeFromNodeName( final String name,
-                                                          final boolean limit_to_five,
                                                           final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction ) {
         if ( ( name.indexOf( "_" ) > 0 )
                 && ( name.length() < 31 )
@@ -234,21 +236,30 @@ public final class ParserUtils {
                 && ( ( ( name.indexOf( "/" ) ) < 0 ) || ( name.indexOf( "/" ) > name.indexOf( "_" ) ) ) ) {
             final String[] s = name.split( "[_/]" );
             if ( s.length > 1 ) {
-                String str = s[ 1 ];
-                if ( ( str.length() < 6 ) || ( !limit_to_five && ( str.length() < 7 ) ) ) {
-                    if ( ( str.length() < 5 ) && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) ) ) {
-                        str = str.substring( 0, 3 );
-                    }
-                    final Matcher uc_letters_and_numbers = NHXParser.UC_LETTERS_NUMBERS_PATTERN.matcher( str );
-                    if ( !uc_letters_and_numbers.matches() ) {
-                        return null;
-                    }
-                    final Matcher numbers_only = NHXParser.NUMBERS_ONLY_PATTERN.matcher( str );
-                    if ( numbers_only.matches() ) {
-                        return null;
-                    }
-                    return str;
+                final String str = s[ 1 ];
+                //   if (  str.length() < 6  ) {
+                if ( ( str.length() < 5 ) && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) ) ) {
+                    return str.substring( 0, 3 );
+                }
+                final Matcher m1 = TAXOMONY_CODE_PATTERN_1.matcher( str );
+                if ( m1.matches() ) {
+                    return m1.group();
+                }
+                final Matcher m2 = TAXOMONY_CODE_PATTERN_2.matcher( str );
+                if ( m2.matches() ) {
+                    return m2.group( 1 );
                 }
+                // return null;
+                //                final Matcher uc_letters_and_numbers = NHXParser.UC_LETTERS_NUMBERS_PATTERN.matcher( str );
+                //                if ( !uc_letters_and_numbers.matches() ) {
+                //                    return null;
+                //                }
+                //                final Matcher numbers_only = NHXParser.NUMBERS_ONLY_PATTERN.matcher( str );
+                //                if ( numbers_only.matches() ) {
+                //                    return null;
+                //                }
+                //                return str;
+                //  }
             }
         }
         return null;

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 94db898..01a4ab6 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -977,12 +977,12 @@ public class PhylogenyMethods {
         if ( !node.getNodeData().isHasTaxonomy() ) {
             return "";
         }
-        if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
-            return node.getNodeData().getTaxonomy().getTaxonomyCode();
-        }
         else if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
             return node.getNodeData().getTaxonomy().getScientificName();
         }
+        if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+            return node.getNodeData().getTaxonomy().getTaxonomyCode();
+        }
         else {
             return node.getNodeData().getTaxonomy().getCommonName();
         }

diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java
index 7ce94fc..780aba9 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDI.java
+++ b/forester/java/src/org/forester/sdi/GSDI.java
@@ -158,10 +158,8 @@ public final class GSDI extends SDI {
         // Determine the sum of traversals.
         int traversals_sum = 0;
         int max_traversals = 0;
-       
         PhylogenyNode max_traversals_node = null;
         if ( !s.isExternal() ) {
-            
             for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
                 final PhylogenyNode current_node = s.getChildNode( i );
                 final int traversals = getTraversalCount( current_node );
@@ -170,7 +168,6 @@ public final class GSDI extends SDI {
                     max_traversals = traversals;
                     max_traversals_node = current_node;
                 }
-               
             }
         }
         // System.out.println( " sum=" + traversals_sum );
@@ -216,15 +213,13 @@ public final class GSDI extends SDI {
         for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
             final PhylogenyNode current_node = s.getChildNode( i );
             final int traversals = getTraversalCount( current_node );
-          
             if ( traversals < min_traversals ) {
                 min_traversals = traversals;
-                
             }
         }
         for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
             final PhylogenyNode current_node = s.getChildNode( i );
-            _transversal_counts.put( current_node, getTraversalCount( current_node  ) - min_traversals );
+            _transversal_counts.put( current_node, getTraversalCount( current_node ) - min_traversals );
         }
     }
 

diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java
index 18ce53f..70655c6 100644 (file)
--- a/forester/java/src/org/forester/sdi/TestGSDI.java
+++ b/forester/java/src/org/forester/sdi/TestGSDI.java
@@ -650,574 +650,574 @@ public final class TestGSDI {
             if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
                 return false;
             }
-                        final Phylogeny g2_23 = TestGSDI
-                                .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
-                        final GSDI sdi2_23 = new GSDI( g2_23, s2, false );
-                        if ( sdi2_23.getDuplicationsSum() != 0 ) {
-                            return false;
-                        }
-                        if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_23.getSpeciationsSum() != 2 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_24 = TestGSDI
-                                .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
-                        final GSDI sdi2_24 = new GSDI( g2_24, s2, false );
-                        if ( sdi2_24.getDuplicationsSum() != 0 ) {
-                            return false;
-                        }
-                        if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_24.getSpeciationsSum() != 2 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_25 = TestGSDI
-                                .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
-                        final GSDI sdi2_25 = new GSDI( g2_25, s2, false );
-                        if ( sdi2_25.getDuplicationsSum() != 0 ) {
-                            return false;
-                        }
-                        if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_25.getSpeciationsSum() != 2 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_26 = TestGSDI
-                                .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
-                        final GSDI sdi2_26 = new GSDI( g2_26, s2, false );
-                        if ( sdi2_26.getDuplicationsSum() != 0 ) {
-                            return false;
-                        }
-                        if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                            return false;
-                        }
-                        if ( sdi2_26.getSpeciationsSum() != 3 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_27 = TestGSDI
-                                .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
-                        final GSDI sdi2_27 = new GSDI( g2_27, s2, false );
-                        if ( sdi2_27.getDuplicationsSum() != 0 ) {
-                            return false;
-                        }
-                        if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_27.getSpeciationsSum() != 2 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_28 = TestGSDI
-                                .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
-                        final GSDI sdi2_28 = new GSDI( g2_28, s2, false );
-                        if ( sdi2_28.getDuplicationsSum() != 0 ) {
-                            return false;
-                        }
-                        if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_28.getSpeciationsSum() != 2 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_29 = TestGSDI
-                                .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
-                        final GSDI sdi2_29 = new GSDI( g2_29, s2, false );
-                        if ( sdi2_29.getDuplicationsSum() != 0 ) {
-                            return false;
-                        }
-                        if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
-                            return false;
-                        }
-                        if ( sdi2_29.getSpeciationsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_30 = TestGSDI
-                                .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
-                        final GSDI sdi2_30 = new GSDI( g2_30, s2, false );
-                        if ( sdi2_30.getDuplicationsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_30.getSpeciationsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_31 = TestGSDI
-                                .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
-                        final GSDI sdi2_31 = new GSDI( g2_31, s2, false );
-                        if ( sdi2_31.getDuplicationsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_31.getSpeciationsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_32 = TestGSDI
-                                .createPhylogeny( "((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
-                        final GSDI sdi2_32 = new GSDI( g2_32, s2, false );
-                        if ( sdi2_32.getDuplicationsSum() != 0 ) {
-                            return false;
-                        }
-                        if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
-                            return false;
-                        }
-                        if ( sdi2_32.getSpeciationsSum() != 3 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
+            final Phylogeny g2_23 = TestGSDI
+                    .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
+            final GSDI sdi2_23 = new GSDI( g2_23, s2, false );
+            if ( sdi2_23.getDuplicationsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_23.getSpeciationsSum() != 2 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_24 = TestGSDI
+                    .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
+            final GSDI sdi2_24 = new GSDI( g2_24, s2, false );
+            if ( sdi2_24.getDuplicationsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_24.getSpeciationsSum() != 2 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_25 = TestGSDI
+                    .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
+            final GSDI sdi2_25 = new GSDI( g2_25, s2, false );
+            if ( sdi2_25.getDuplicationsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_25.getSpeciationsSum() != 2 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_26 = TestGSDI
+                    .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
+            final GSDI sdi2_26 = new GSDI( g2_26, s2, false );
+            if ( sdi2_26.getDuplicationsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi2_26.getSpeciationsSum() != 3 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
+                return false;
+            }
+            final Phylogeny g2_27 = TestGSDI
+                    .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
+            final GSDI sdi2_27 = new GSDI( g2_27, s2, false );
+            if ( sdi2_27.getDuplicationsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_27.getSpeciationsSum() != 2 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_28 = TestGSDI
+                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
+            final GSDI sdi2_28 = new GSDI( g2_28, s2, false );
+            if ( sdi2_28.getDuplicationsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_28.getSpeciationsSum() != 2 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
+                return false;
+            }
+            final Phylogeny g2_29 = TestGSDI
+                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
+            final GSDI sdi2_29 = new GSDI( g2_29, s2, false );
+            if ( sdi2_29.getDuplicationsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
+                return false;
+            }
+            if ( sdi2_29.getSpeciationsSum() != 1 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_30 = TestGSDI
+                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
+            final GSDI sdi2_30 = new GSDI( g2_30, s2, false );
+            if ( sdi2_30.getDuplicationsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_30.getSpeciationsSum() != 1 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_31 = TestGSDI
+                    .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
+            final GSDI sdi2_31 = new GSDI( g2_31, s2, false );
+            if ( sdi2_31.getDuplicationsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_31.getSpeciationsSum() != 1 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_32 = TestGSDI
+                    .createPhylogeny( "((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
+            final GSDI sdi2_32 = new GSDI( g2_32, s2, false );
+            if ( sdi2_32.getDuplicationsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
+                return false;
+            }
+            if ( sdi2_32.getSpeciationsSum() != 3 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
             //            //-
-                        final Phylogeny g2_33_d = TestGSDI
-                                .createPhylogeny( "((((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?],(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?])" );
-                        final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false );
-                        Archaeopteryx.createApplication( g2_33_d );
-                        //  Archaeopteryx.createApplication( s2 );
-                        //-
-                        final Phylogeny g2_33 = TestGSDI
-                                .createPhylogeny( "(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),k2[&&NHX:S=k2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
-                        final GSDI sdi2_33 = new GSDI( g2_33, s2, false );
-                        Archaeopteryx.createApplication( g2_33 );
-                        // Archaeopteryx.createApplication( s2 );
-                        if ( sdi2_33.getDuplicationsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
-                            return false;
-                        }
-                        if ( sdi2_33.getSpeciationsSum() != 3 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_34 = TestGSDI
-                                .createPhylogeny( "(((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4])" );
-                        final GSDI sdi2_34 = new GSDI( g2_34, s2, false );
-                        if ( sdi2_34.getDuplicationsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_34.getSpeciationsSum() != 2 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_35 = TestGSDI
-                                .createPhylogeny( "((((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4]),a1_0[&&NHX:S=a1])" );
-                        final GSDI sdi2_35 = new GSDI( g2_35, s2, false );
-                        if ( sdi2_35.getDuplicationsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_35.getSpeciationsSum() != 3 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_36 = TestGSDI
-                                .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a1_1[&&NHX:S=a1],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
-                        final GSDI sdi2_36 = new GSDI( g2_36, s2, false );
-                        if ( sdi2_36.getDuplicationsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_36.getSpeciationsSum() != 2 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_37 = TestGSDI
-                                .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a2_0[&&NHX:S=a2],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
-                        final GSDI sdi2_37 = new GSDI( g2_37, s2, false );
-                        if ( sdi2_37.getDuplicationsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_37.getSpeciationsSum() != 2 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_38 = TestGSDI
-                                .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
-                        final GSDI sdi2_38 = new GSDI( g2_38, s2, false );
-                        if ( sdi2_38.getDuplicationsSum() != 5 ) {
-                            return false;
-                        }
-                        if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                            return false;
-                        }
-                        if ( sdi2_38.getSpeciationsSum() != 0 ) {
-                            return false;
-                        }
-                        final Phylogeny g2_100 = TestGSDI
-                                .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],h2[&&NHX:S=h2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],b1[&&NHX:S=b1])))" );
-                        final GSDI sdi2_100 = new GSDI( g2_100, s2, false );
-                        if ( sdi2_100.getDuplicationsSum() != 4 ) {
-                            return false;
-                        }
-                        if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
-                            return false;
-                        }
-                        if ( sdi2_100.getSpeciationsSum() != 4 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny g2_101 = TestGSDI
-                                .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],b2[&&NHX:S=b2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],j1[&&NHX:S=j1])))" );
-                        final GSDI sdi2_101 = new GSDI( g2_101, s2, false );
-                        if ( sdi2_101.getDuplicationsSum() != 2 ) {
-                            return false;
-                        }
-                        if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
-                            return false;
-                        }
-                        if ( sdi2_101.getSpeciationsSum() != 5 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
-                            return false;
-                        }
-                        final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
-                        DevelopmentTools.numberSpeciesInOrder( s_7_4 );
-                        final Phylogeny g_7_4_1 = TestGSDI
-                                .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
-                                        + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
-                                        + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
-                                        + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
-                                        + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
-                                        + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
-                                        + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
-                                        + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
-                                        + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
-                                        + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
-                                        + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
-                                        + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
-                        final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false );
-                        if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
-                            return false;
-                        }
-                        if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
-                            return false;
-                        }
-                        if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
-                            return false;
-                        }
-                        if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
-                            return false;
-                        }
-                        final Phylogeny g_7_4_2 = TestGSDI
-                                .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
-                                        + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
-                                        + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
-                                        + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
-                                        + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
-                                        + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
-                                        + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
-                                        + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
-                                        + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
-                                        + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
-                                        + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
-                                        + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
-                                        + "66[&&NHX:S=66]),257[&&NHX:S=257]),258[&&NHX:S=258]),513[&&NHX:S=513]),514[&&NHX:S=514]),769[&&NHX:S=769]),770[&&NHX:S=770])" );
-                        final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false );
-                        if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
-                            return false;
-                        }
-                        if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
-                            return false;
-                        }
-                        if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
-                            return false;
-                        }
+            final Phylogeny g2_33_d = TestGSDI
+                    .createPhylogeny( "((((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?],(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?])" );
+            final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false );
+            Archaeopteryx.createApplication( g2_33_d );
+            //  Archaeopteryx.createApplication( s2 );
+            //-
+            final Phylogeny g2_33 = TestGSDI
+                    .createPhylogeny( "(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),k2[&&NHX:S=k2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
+            final GSDI sdi2_33 = new GSDI( g2_33, s2, false );
+            Archaeopteryx.createApplication( g2_33 );
+            // Archaeopteryx.createApplication( s2 );
+            if ( sdi2_33.getDuplicationsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
+                return false;
+            }
+            if ( sdi2_33.getSpeciationsSum() != 3 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_34 = TestGSDI
+                    .createPhylogeny( "(((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4])" );
+            final GSDI sdi2_34 = new GSDI( g2_34, s2, false );
+            if ( sdi2_34.getDuplicationsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_34.getSpeciationsSum() != 2 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_35 = TestGSDI
+                    .createPhylogeny( "((((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4]),a1_0[&&NHX:S=a1])" );
+            final GSDI sdi2_35 = new GSDI( g2_35, s2, false );
+            if ( sdi2_35.getDuplicationsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_35.getSpeciationsSum() != 3 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
+                return false;
+            }
+            final Phylogeny g2_36 = TestGSDI
+                    .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a1_1[&&NHX:S=a1],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
+            final GSDI sdi2_36 = new GSDI( g2_36, s2, false );
+            if ( sdi2_36.getDuplicationsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_36.getSpeciationsSum() != 2 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_37 = TestGSDI
+                    .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a2_0[&&NHX:S=a2],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
+            final GSDI sdi2_37 = new GSDI( g2_37, s2, false );
+            if ( sdi2_37.getDuplicationsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_37.getSpeciationsSum() != 2 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_38 = TestGSDI
+                    .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
+            final GSDI sdi2_38 = new GSDI( g2_38, s2, false );
+            if ( sdi2_38.getDuplicationsSum() != 5 ) {
+                return false;
+            }
+            if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi2_38.getSpeciationsSum() != 0 ) {
+                return false;
+            }
+            final Phylogeny g2_100 = TestGSDI
+                    .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],h2[&&NHX:S=h2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],b1[&&NHX:S=b1])))" );
+            final GSDI sdi2_100 = new GSDI( g2_100, s2, false );
+            if ( sdi2_100.getDuplicationsSum() != 4 ) {
+                return false;
+            }
+            if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
+                return false;
+            }
+            if ( sdi2_100.getSpeciationsSum() != 4 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
+                return false;
+            }
+            final Phylogeny g2_101 = TestGSDI
+                    .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],b2[&&NHX:S=b2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],j1[&&NHX:S=j1])))" );
+            final GSDI sdi2_101 = new GSDI( g2_101, s2, false );
+            if ( sdi2_101.getDuplicationsSum() != 2 ) {
+                return false;
+            }
+            if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
+                return false;
+            }
+            if ( sdi2_101.getSpeciationsSum() != 5 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
+                return false;
+            }
+            final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
+            DevelopmentTools.numberSpeciesInOrder( s_7_4 );
+            final Phylogeny g_7_4_1 = TestGSDI
+                    .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
+                            + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
+                            + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
+                            + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
+                            + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
+                            + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
+                            + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
+                            + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
+                            + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
+                            + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
+                            + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
+                            + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
+            final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false );
+            if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
+                return false;
+            }
+            if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
+                return false;
+            }
+            if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
+                return false;
+            }
+            if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
+                return false;
+            }
+            final Phylogeny g_7_4_2 = TestGSDI
+                    .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
+                            + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
+                            + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
+                            + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
+                            + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
+                            + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
+                            + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
+                            + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
+                            + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
+                            + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
+                            + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
+                            + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
+                            + "66[&&NHX:S=66]),257[&&NHX:S=257]),258[&&NHX:S=258]),513[&&NHX:S=513]),514[&&NHX:S=514]),769[&&NHX:S=769]),770[&&NHX:S=770])" );
+            final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false );
+            if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
+                return false;
+            }
+            if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
+                return false;
+            }
+            if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
+                return false;
+            }
             //---------------------
-//             final String g2_0_ =
-//             "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
-//             final Phylogeny g2_0 = factory.create( g2_0_, new NHXParser() )[
-//             0 ];
-//             g2_0.setRooted( true );
-//             final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
-//             if ( sdi2_0.getDuplicationsSum() != 0 ) {
-//             return false;
-//             }
-//             final String g2_1_= "";
-//             final Phylogeny g2_1 = factory.create( g2_1_, new NHXParser() )[
-//             0 ];
-//             g2_1.setRooted( true );
-//             final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
-//             if ( sdi2_1.getDuplicationsSum() != 0 ) {
-//             return false;
-//             }
+            //             final String g2_0_ =
+            //             "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
+            //             final Phylogeny g2_0 = factory.create( g2_0_, new NHXParser() )[
+            //             0 ];
+            //             g2_0.setRooted( true );
+            //             final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
+            //             if ( sdi2_0.getDuplicationsSum() != 0 ) {
+            //             return false;
+            //             }
+            //             final String g2_1_= "";
+            //             final Phylogeny g2_1 = factory.create( g2_1_, new NHXParser() )[
+            //             0 ];
+            //             g2_1.setRooted( true );
+            //             final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
+            //             if ( sdi2_1.getDuplicationsSum() != 0 ) {
+            //             return false;
+            //             }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index d1ab3bb..452be95 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -2123,7 +2123,7 @@ public final class Test {
                 return false;
             }
             t2.setIdentifier( new Identifier( "ecoli" ) );
-            t2.setTaxonomyCode( "other" );
+            t2.setTaxonomyCode( "OTHER" );
             t2.setScientificName( "what" );
             t2.setCommonName( "something" );
             if ( !t1.isEqual( t2 ) ) {
@@ -4706,69 +4706,81 @@ public final class Test {
             if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
                 return false;
             }
-            if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
-                final PhylogenyNode a = PhylogenyNode
-                        .createInstanceFromNhxString( "n10_ECOLI/1-2",
-                                                      PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
-                if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
-                    return false;
-                }
-                if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
-                    return false;
-                }
-                final PhylogenyNode b = PhylogenyNode
-                        .createInstanceFromNhxString( "n10_ECOLI1/1-2",
-                                                      PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
-                if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
-                    return false;
-                }
-                if ( !PhylogenyMethods.getSpecies( b ).equals( "" ) ) {
-                    return false;
-                }
-                final PhylogenyNode c = PhylogenyNode
-                        .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
-                                                      PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
-                if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
-                    return false;
-                }
-                if ( !PhylogenyMethods.getSpecies( c ).equals( "" ) ) {
-                    return false;
-                }
-                final PhylogenyNode c1 = PhylogenyNode
-                        .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
-                                                      PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
-                if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
-                    return false;
-                }
-                if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
-                    return false;
-                }
-                final PhylogenyNode c2 = PhylogenyNode
-                        .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
-                                                      PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
-                if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
-                    return false;
-                }
-                if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
-                    return false;
-                }
-                final PhylogenyNode d = PhylogenyNode
-                        .createInstanceFromNhxString( "n10_RAT1/1-2",
-                                                      PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
-                if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
-                    return false;
-                }
-                if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
-                    return false;
-                }
-                final PhylogenyNode e = PhylogenyNode
-                        .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
-                if ( !e.getName().equals( "n10_RAT1" ) ) {
-                    return false;
-                }
-                if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
-                    return false;
-                }
+            final PhylogenyNode a = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+            if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
+                return false;
+            }
+            final PhylogenyNode b = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_ECOLI1/1-2",
+                                                  PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+            if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
+                return false;
+            }
+            final PhylogenyNode c = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
+                                                  PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+            if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
+                return false;
+            }
+            final PhylogenyNode c1 = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
+                                                  PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+            if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
+                return false;
+            }
+            final PhylogenyNode c2 = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
+                                                  PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+            if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
+                return false;
+            }
+            final PhylogenyNode d = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_RAT1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+            if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
+                return false;
+            }
+            final PhylogenyNode e = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+            if ( !e.getName().equals( "n10_RAT1" ) ) {
+                return false;
+            }
+            if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
+                return false;
+            }
+            final PhylogenyNode e2 = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
+            if ( !e2.getName().equals( "n10_RAT1" ) ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
+                return false;
+            }
+            final PhylogenyNode e3 = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_RAT~", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
+            if ( !e3.getName().equals( "n10_RAT~" ) ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
+                return false;
             }
             final PhylogenyNode n11 = PhylogenyNode
                     .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
@@ -4794,6 +4806,22 @@ public final class Test {
             if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
                 return false;
             }
+            final PhylogenyNode m = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_MOUSEa", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
+            if ( !m.getName().equals( "n10_MOUSEa" ) ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
+                return false;
+            }
+            final PhylogenyNode o = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_MOUSE_", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
+            if ( !o.getName().equals( "n10_MOUSE_" ) ) {
+                return false;
+            }
+            if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
+                return false;
+            }
             final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
             final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
             if ( !tvu1.getRef().equals( "tag1" ) ) {
@@ -4878,7 +4906,7 @@ public final class Test {
             if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
                 return false;
             }
-            if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
+            if ( !PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
                 return false;
             }
             final PhylogenyNode n14 = PhylogenyNode