X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=a57974a4ff0c623498da0210ad3dc5102052b80e;hb=d15038d8870ccccd726ad82ac9a707afb6a7f31e;hp=796acd06d035a8f4d9b5dd1caeb0c5af6106bf01;hpb=7bbb45295594e9574ee64a32fac17a93b5aa6ade;p=jalview.git

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 796acd0..a57974a 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -36,6 +36,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Locale;
 import java.util.Set;
+import java.util.SortedSet;
 
 import org.forester.application.support_transfer;
 import org.forester.archaeopteryx.TreePanelUtil;
@@ -70,6 +71,7 @@ import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.Accession.Source;
 import org.forester.phylogeny.data.BinaryCharacters;
 import org.forester.phylogeny.data.BranchWidth;
 import org.forester.phylogeny.data.Confidence;
@@ -113,7 +115,7 @@ import org.forester.util.DescriptiveStatistics;
 import org.forester.util.ForesterConstants;
 import org.forester.util.ForesterUtil;
 import org.forester.util.GeneralTable;
-import org.forester.util.SequenceIdParser;
+import org.forester.util.SequenceAccessionTools;
 import org.forester.ws.seqdb.SequenceDatabaseEntry;
 import org.forester.ws.seqdb.SequenceDbWsTools;
 import org.forester.ws.seqdb.UniProtTaxonomy;
@@ -125,6 +127,7 @@ import org.forester.ws.wabi.TxSearch.TAX_RANK;
 @SuppressWarnings( "unused")
 public final class Test {
 
+    private final static boolean PERFORM_DB_TESTS          = false;
     private final static double  ZERO_DIFF                 = 1.0E-9;
     private final static String  PATH_TO_TEST_DATA         = System.getProperty( "user.dir" )
                                                                    + ForesterUtil.getFileSeparator() + "test_data"
@@ -140,6 +143,259 @@ public final class Test {
                                                                    + ForesterConstants.PHYLO_XML_VERSION + "/"
                                                                    + ForesterConstants.PHYLO_XML_XSD;
 
+    public 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 );
+            final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
+            final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
+            final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
+            final List<Boolean> covered = new ArrayList<Boolean>();
+            covered.add( true ); // 0
+            covered.add( false ); // 1
+            covered.add( true ); // 2
+            covered.add( false ); // 3
+            covered.add( true ); // 4
+            covered.add( true ); // 5
+            covered.add( false ); // 6
+            covered.add( true ); // 7
+            covered.add( true ); // 8
+            if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) {
+                return false;
+            }
+            if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) {
+                return false;
+            }
+            if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) {
+                return false;
+            }
+            if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) {
+                return false;
+            }
+            if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) {
+                return false;
+            }
+            final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.01, 1 );
+            final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
+            final Protein ab = new BasicProtein( "ab", "varanus", 0 );
+            ab.addProteinDomain( a );
+            ab.addProteinDomain( b );
+            final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab );
+            if ( ab.getNumberOfProteinDomains() != 2 ) {
+                return false;
+            }
+            if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
+                return false;
+            }
+            if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
+                return false;
+            }
+            final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
+            if ( ab.getNumberOfProteinDomains() != 2 ) {
+                return false;
+            }
+            if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
+                return false;
+            }
+            final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
+            final Domain d = new BasicDomain( "d",
+                                              ( short ) 10000,
+                                              ( short ) 10500,
+                                              ( short ) 1,
+                                              ( short ) 1,
+                                              0.0000001,
+                                              1 );
+            final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
+            final Protein cde = new BasicProtein( "cde", "varanus", 0 );
+            cde.addProteinDomain( c );
+            cde.addProteinDomain( d );
+            cde.addProteinDomain( e );
+            final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde );
+            if ( cde.getNumberOfProteinDomains() != 3 ) {
+                return false;
+            }
+            if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
+                return false;
+            }
+            final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
+            final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
+            final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
+            final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
+            final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
+            final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
+            fghi.addProteinDomain( f );
+            fghi.addProteinDomain( g );
+            fghi.addProteinDomain( h );
+            fghi.addProteinDomain( i );
+            fghi.addProteinDomain( i );
+            fghi.addProteinDomain( i );
+            fghi.addProteinDomain( i2 );
+            final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi );
+            if ( fghi.getNumberOfProteinDomains() != 7 ) {
+                return false;
+            }
+            if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
+                return false;
+            }
+            if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
+                return false;
+            }
+            final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi );
+            if ( fghi.getNumberOfProteinDomains() != 7 ) {
+                return false;
+            }
+            if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
+                return false;
+            }
+            final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
+            final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
+            final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
+            final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
+            final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
+            final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
+            final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
+            final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
+            jklm.addProteinDomain( j );
+            jklm.addProteinDomain( k );
+            jklm.addProteinDomain( l );
+            jklm.addProteinDomain( m );
+            jklm.addProteinDomain( m0 );
+            jklm.addProteinDomain( m1 );
+            jklm.addProteinDomain( m2 );
+            final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm );
+            if ( jklm.getNumberOfProteinDomains() != 7 ) {
+                return false;
+            }
+            if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
+                return false;
+            }
+            if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
+                return false;
+            }
+            final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm );
+            if ( jklm.getNumberOfProteinDomains() != 7 ) {
+                return false;
+            }
+            if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
+                return false;
+            }
+            final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
+            final Protein od = new BasicProtein( "od", "varanus", 0 );
+            od.addProteinDomain( only );
+            final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od );
+            if ( od.getNumberOfProteinDomains() != 1 ) {
+                return false;
+            }
+            if ( od_s0.getNumberOfProteinDomains() != 1 ) {
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+
+    public 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 );
+            final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
+            final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
+            final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
+            final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
+            final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
+            final List<Boolean> covered = new ArrayList<Boolean>();
+            covered.add( true ); // 0
+            covered.add( false ); // 1
+            covered.add( true ); // 2
+            covered.add( false ); // 3
+            covered.add( true ); // 4
+            covered.add( true ); // 5
+            covered.add( false ); // 6
+            covered.add( true ); // 7
+            covered.add( true ); // 8
+            if ( ForesterUtil.isEngulfed( d0, covered ) ) {
+                return false;
+            }
+            if ( ForesterUtil.isEngulfed( d1, covered ) ) {
+                return false;
+            }
+            if ( ForesterUtil.isEngulfed( d2, covered ) ) {
+                return false;
+            }
+            if ( !ForesterUtil.isEngulfed( d3, covered ) ) {
+                return false;
+            }
+            if ( ForesterUtil.isEngulfed( d4, covered ) ) {
+                return false;
+            }
+            if ( ForesterUtil.isEngulfed( d5, covered ) ) {
+                return false;
+            }
+            if ( !ForesterUtil.isEngulfed( d6, covered ) ) {
+                return false;
+            }
+            final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
+            final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
+            final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
+            final Protein abc = new BasicProtein( "abc", "nemve", 0 );
+            abc.addProteinDomain( a );
+            abc.addProteinDomain( b );
+            abc.addProteinDomain( c );
+            final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc );
+            final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc );
+            if ( abc.getNumberOfProteinDomains() != 3 ) {
+                return false;
+            }
+            if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
+                return false;
+            }
+            if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
+                return false;
+            }
+            if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
+                return false;
+            }
+            if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
+                return false;
+            }
+            final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
+            final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
+            final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
+            final Protein def = new BasicProtein( "def", "nemve", 0 );
+            def.addProteinDomain( d );
+            def.addProteinDomain( e );
+            def.addProteinDomain( f );
+            final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def );
+            final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def );
+            if ( def.getNumberOfProteinDomains() != 3 ) {
+                return false;
+            }
+            if ( def_r1.getNumberOfProteinDomains() != 3 ) {
+                return false;
+            }
+            if ( def_r2.getNumberOfProteinDomains() != 3 ) {
+                return false;
+            }
+            if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
+                return false;
+            }
+            if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
+                return false;
+            }
+            if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+
     public static boolean isEqual( final double a, final double b ) {
         return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
     }
@@ -171,6 +427,15 @@ 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." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
         System.out.print( "Protein id: " );
         if ( !testProteinId() ) {
             System.out.println( "failed." );
@@ -225,8 +490,20 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        System.out.print( "Hmmscan output parser: " );
-        if ( testHmmscanOutputParser() ) {
+        if ( PERFORM_DB_TESTS ) {
+            System.out.print( "Ebi Entry Retrieval: " );
+            if ( Test.testEbiEntryRetrieval() ) {
+                System.out.println( "OK." );
+                succeeded++;
+            }
+            else {
+                System.out.println( "failed." );
+                failed++;
+            }
+        }
+        ///////////////////////////////////////// System.exit( 0 );
+        System.out.print( "UniProtKB id extraction: " );
+        if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
             System.out.println( "OK." );
             succeeded++;
         }
@@ -234,8 +511,8 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        System.out.print( "Basic node methods: " );
-        if ( Test.testBasicNodeMethods() ) {
+        System.out.print( "Sequence DB tools 1: " );
+        if ( testSequenceDbWsTools1() ) {
             System.out.println( "OK." );
             succeeded++;
         }
@@ -243,8 +520,20 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        System.out.print( "Taxonomy code extraction: " );
-        if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
+        if ( PERFORM_DB_TESTS ) {
+            System.out.print( "Sequence DB tools 2: " );
+            if ( testSequenceDbWsTools2() ) {
+                System.out.println( "OK." );
+                succeeded++;
+            }
+            else {
+                System.out.println( "failed." );
+                failed++;
+                System.exit( -1 );
+            }
+        }
+        System.out.print( "Hmmscan output parser: " );
+        if ( testHmmscanOutputParser() ) {
             System.out.println( "OK." );
             succeeded++;
         }
@@ -252,8 +541,28 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        System.out.print( "SN extraction: " );
-        if ( Test.testExtractSNFromNodeName() ) {
+        //
+        System.out.print( "Overlap removal: " );
+        if ( !org.forester.test.Test.testOverlapRemoval() ) {
+            System.out.println( "failed." );
+            failed++;
+        }
+        else {
+            succeeded++;
+        }
+        System.out.println( "OK." );
+        System.out.print( "Engulfing overlap removal: " );
+        if ( !Test.testEngulfingOverlapRemoval() ) {
+            System.out.println( "failed." );
+            failed++;
+        }
+        else {
+            succeeded++;
+        }
+        System.out.println( "OK." );
+        //
+        System.out.print( "Taxonomy code extraction: " );
+        if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
             System.out.println( "OK." );
             succeeded++;
         }
@@ -261,8 +570,8 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        System.out.print( "Taxonomy extraction (general): " );
-        if ( Test.testTaxonomyExtraction() ) {
+        System.out.print( "SN extraction: " );
+        if ( Test.testExtractSNFromNodeName() ) {
             System.out.println( "OK." );
             succeeded++;
         }
@@ -270,8 +579,8 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        System.out.print( "UniProtKB id extraction: " );
-        if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
+        System.out.print( "Taxonomy extraction (general): " );
+        if ( Test.testTaxonomyExtraction() ) {
             System.out.println( "OK." );
             succeeded++;
         }
@@ -450,6 +759,15 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
+        System.out.print( "Tree copy: " );
+        if ( Test.testTreeCopy() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
         System.out.print( "Basic tree methods: " );
         if ( Test.testBasicTreeMethods() ) {
             System.out.println( "OK." );
@@ -804,17 +1122,8 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        System.out.print( "EMBL Entry Retrieval: " );
-        if ( Test.testEmblEntryRetrieval() ) {
-            System.out.println( "OK." );
-            succeeded++;
-        }
-        else {
-            System.out.println( "failed." );
-            failed++;
-        }
-        System.out.print( "Uniprot Entry Retrieval: " );
-        if ( Test.testUniprotEntryRetrieval() ) {
+        System.out.print( "Genbank accessor parsing: " );
+        if ( Test.testGenbankAccessorParsing() ) {
             System.out.println( "OK." );
             succeeded++;
         }
@@ -822,14 +1131,27 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        System.out.print( "Uniprot Taxonomy Search: " );
-        if ( Test.testUniprotTaxonomySearch() ) {
-            System.out.println( "OK." );
-            succeeded++;
+        if ( PERFORM_DB_TESTS ) {
+            System.out.print( "Uniprot Entry Retrieval: " );
+            if ( Test.testUniprotEntryRetrieval() ) {
+                System.out.println( "OK." );
+                succeeded++;
+            }
+            else {
+                System.out.println( "failed." );
+                failed++;
+            }
         }
-        else {
-            System.out.println( "failed." );
-            failed++;
+        if ( PERFORM_DB_TESTS ) {
+            System.out.print( "Uniprot Taxonomy Search: " );
+            if ( Test.testUniprotTaxonomySearch() ) {
+                System.out.println( "OK." );
+                succeeded++;
+            }
+            else {
+                System.out.println( "failed." );
+                failed++;
+            }
         }
         //----
         String path = "";
@@ -1208,6 +1530,22 @@ public final class Test {
             if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
                 return false;
             }
+            final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
+            if ( x.size() != 4 ) {
+                return false;
+            }
+            int c = 0;
+            for( final Accession acc : x ) {
+                if ( c == 0 ) {
+                    if ( !acc.getSource().equals( "KEGG" ) ) {
+                        return false;
+                    }
+                    if ( !acc.getValue().equals( "hsa:596" ) ) {
+                        return false;
+                    }
+                }
+                c++;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );
@@ -1487,7 +1825,6 @@ public final class Test {
             }
             if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
                     .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
-                ;
                 return false;
             }
             if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
@@ -1536,6 +1873,23 @@ public final class Test {
                     .equalsIgnoreCase( "433" ) ) {
                 return false;
             }
+            final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
+                    .getCrossReferences();
+            if ( x.size() != 4 ) {
+                return false;
+            }
+            int c = 0;
+            for( final Accession acc : x ) {
+                if ( c == 0 ) {
+                    if ( !acc.getSource().equals( "KEGG" ) ) {
+                        return false;
+                    }
+                    if ( !acc.getValue().equals( "hsa:596" ) ) {
+                        return false;
+                    }
+                }
+                c++;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );
@@ -2420,6 +2774,41 @@ public final class Test {
         return true;
     }
 
+    private static boolean testTreeCopy() {
+        try {
+            final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
+            final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
+            final Phylogeny t1 = t0.copy();
+            if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
+                return false;
+            }
+            if ( !t1.toNewHampshireX().equals( str_0 ) ) {
+                return false;
+            }
+            t0.deleteSubtree( t0.getNode( "c" ), true );
+            t0.deleteSubtree( t0.getNode( "a" ), true );
+            t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
+            t0.getNode( "b" ).setName( "Bee" );
+            if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
+                return false;
+            }
+            if ( !t1.toNewHampshireX().equals( str_0 ) ) {
+                return false;
+            }
+            t0.deleteSubtree( t0.getNode( "e" ), true );
+            t0.deleteSubtree( t0.getNode( "Bee" ), true );
+            t0.deleteSubtree( t0.getNode( "d" ), true );
+            if ( !t1.toNewHampshireX().equals( str_0 ) ) {
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace();
+            return false;
+        }
+        return true;
+    }
+
     private static boolean testCreateBalancedPhylogeny() {
         try {
             final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
@@ -2471,8 +2860,8 @@ public final class Test {
             if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
                 return false;
             }
-            n.setName( "j40f4_Q06891.1_fndn2 fnr3" );
-            if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "Q06891.1" ) ) {
+            n.setName( "AAA34956" );
+            if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
                 return false;
             }
             n.setName( "GI:394892" );
@@ -2490,6 +2879,16 @@ public final class Test {
                 System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
                 return false;
             }
+            n.setName( "P12345" );
+            if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
+                System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
+                return false;
+            }
+            n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" );
+            if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
+                System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );
@@ -3291,51 +3690,51 @@ public final class Test {
         return true;
     }
 
-    private static boolean testEmblEntryRetrieval() {
+    private static boolean testGenbankAccessorParsing() {
         //The format for GenBank Accession numbers are:
         //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
         //Protein:    3 letters + 5 numerals
         //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
-        if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
+        if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
             return false;
         }
-        if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861.2" ).equals( "AY423861.2" ) ) {
+        if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
             return false;
         }
-        if ( !SequenceIdParser.parseGenbankAccessor( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
+        if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
             return false;
         }
-        if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
+        if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
             return false;
         }
-        if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
+        if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
             return false;
         }
-        if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
+        if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
             return false;
         }
-        if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
+        if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
             return false;
         }
-        if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
+        if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
             return false;
         }
-        if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
+        if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
             return false;
         }
-        if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
+        if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
             return false;
         }
-        if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
+        if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
             return false;
         }
-        if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
+        if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
             return false;
         }
-        if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
+        if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
             return false;
         }
-        if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
+        if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
             return false;
         }
         return true;
@@ -3629,166 +4028,166 @@ public final class Test {
         try {
             PhylogenyNode n = new PhylogenyNode();
             n.setName( "tr|B3RJ64" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( "tr.B3RJ64" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( "tr=B3RJ64" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( "tr-B3RJ64" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( "tr/B3RJ64" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( "tr\\B3RJ64" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( "tr_B3RJ64" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( " tr|B3RJ64 " );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( "-tr|B3RJ64-" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( "-tr=B3RJ64-" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( "_tr=B3RJ64_" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( " tr_tr|B3RJ64_sp|123 " );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
-            n.setName( "sp|B3RJ64" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            n.setName( "B3RJ64" );
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
-            n.setName( "ssp|B3RJ64" );
-            if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+            n.setName( "sp|B3RJ64" );
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( "sp|B3RJ64C" );
-            if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+            if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
                 return false;
             }
             n.setName( "sp B3RJ64" );
-            if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n.setName( "sp|B3RJ6X" );
-            if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+            if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
                 return false;
             }
             n.setName( "sp|B3RJ6" );
-            if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+            if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
                 return false;
             }
             n.setName( "K1PYK7_CRAGI" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
                 return false;
             }
             n.setName( "K1PYK7_PEA" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PEA" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
                 return false;
             }
             n.setName( "K1PYK7_RAT" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_RAT" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
                 return false;
             }
             n.setName( "K1PYK7_PIG" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
                 return false;
             }
             n.setName( "~K1PYK7_PIG~" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
                 return false;
             }
             n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
                 return false;
             }
             n.setName( "K1PYKX_CRAGI" );
-            if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+            if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
                 return false;
             }
             n.setName( "XXXXX_CRAGI" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "XXXXX_CRAGI" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
                 return false;
             }
             n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "H3IB65" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
                 return false;
             }
             n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
-            if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+            if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
                 return false;
             }
             n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "Q86U06" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
                 return false;
             }
             n = new PhylogenyNode();
             org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
             seq.setSymbol( "K1PYK7_CRAGI" );
             n.getNodeData().addSequence( seq );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
                 return false;
             }
             seq.setSymbol( "tr|B3RJ64" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n = new PhylogenyNode();
             seq = new org.forester.phylogeny.data.Sequence();
             seq.setName( "K1PYK7_CRAGI" );
             n.getNodeData().addSequence( seq );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
                 return false;
             }
             seq.setName( "tr|B3RJ64" );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             n = new PhylogenyNode();
             seq = new org.forester.phylogeny.data.Sequence();
             seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
             n.getNodeData().addSequence( seq );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK8_CRAGI" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
                 return false;
             }
             n = new PhylogenyNode();
             seq = new org.forester.phylogeny.data.Sequence();
             seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
             n.getNodeData().addSequence( seq );
-            if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+            if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
                 return false;
             }
             //
             n = new PhylogenyNode();
             n.setName( "ACP19736" );
-            if ( !ForesterUtil.extractGenbankAccessor( n ).equals( "ACP19736" ) ) {
+            if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
                 return false;
             }
             n = new PhylogenyNode();
-            n.setName( "_ACP19736_" );
-            if ( !ForesterUtil.extractGenbankAccessor( n ).equals( "ACP19736" ) ) {
+            n.setName( "|ACP19736|" );
+            if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
                 return false;
             }
         }
@@ -9587,123 +9986,111 @@ public final class Test {
 
     private static boolean testSequenceIdParsing() {
         try {
-            Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
-            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
-                    || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
+            Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
-                    System.out.println( "provider=" + id.getProvider() );
+                    System.out.println( "provider=" + id.getSource() );
                 }
                 return false;
             }
             //
-            id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
-            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
-                    || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
+            id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
-                    System.out.println( "provider=" + id.getProvider() );
+                    System.out.println( "provider=" + id.getSource() );
                 }
                 return false;
             }
             //
-            id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
-            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
-                    || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
+            id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
-                    System.out.println( "provider=" + id.getProvider() );
+                    System.out.println( "provider=" + id.getSource() );
                 }
                 return false;
             }
             // 
-            id = SequenceIdParser.parse( "gb_AAA96518_1" );
-            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
-                    || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
+            id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
-                    System.out.println( "provider=" + id.getProvider() );
+                    System.out.println( "provider=" + id.getSource() );
                 }
                 return false;
             }
             // 
-            id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
-            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
-                    || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
+            id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
-                    System.out.println( "provider=" + id.getProvider() );
+                    System.out.println( "provider=" + id.getSource() );
                 }
                 return false;
             }
             // 
-            id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
-            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
-                    || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
+            id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
-                    System.out.println( "provider=" + id.getProvider() );
+                    System.out.println( "provider=" + id.getSource() );
                 }
                 return false;
             }
             // 
-            id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
-            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
-                    || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
+            id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
-                    System.out.println( "provider=" + id.getProvider() );
+                    System.out.println( "provider=" + id.getSource() );
                 }
                 return false;
             }
             // 
-            id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
-            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
-                    || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
+            id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
-                    System.out.println( "provider=" + id.getProvider() );
+                    System.out.println( "provider=" + id.getSource() );
                 }
                 return false;
             }
             // 
-            id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
-            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
-                    || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
+            id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
-                    System.out.println( "provider=" + id.getProvider() );
+                    System.out.println( "provider=" + id.getSource() );
                 }
                 return false;
             }
             // 
-            id = SequenceIdParser.parse( "P4A123" );
-            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
-                    || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
+            id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
+            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+                    || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
-                    System.out.println( "provider=" + id.getProvider() );
+                    System.out.println( "provider=" + id.getSource() );
                 }
                 return false;
             }
-            // 
-            id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
-            if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
-                    || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
-                if ( id != null ) {
-                    System.out.println( "value   =" + id.getValue() );
-                    System.out.println( "provider=" + id.getProvider() );
-                }
-                return false;
-            }
-            // 
-            id = SequenceIdParser.parse( "XP_12345" );
+            id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
             if ( id != null ) {
                 System.out.println( "value   =" + id.getValue() );
-                System.out.println( "provider=" + id.getProvider() );
+                System.out.println( "provider=" + id.getSource() );
                 return false;
             }
-            // lcl_91970_unknown_
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );
@@ -10806,6 +11193,344 @@ public final class Test {
         return true;
     }
 
+    private static boolean testSequenceDbWsTools1() {
+        try {
+            final PhylogenyNode n = new PhylogenyNode();
+            n.setName( "NP_001025424" );
+            Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
+                    || !acc.getValue().equals( "NP_001025424" ) ) {
+                return false;
+            }
+            n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
+                    || !acc.getValue().equals( "NP_001025424" ) ) {
+                return false;
+            }
+            n.setName( "NP_001025424.1" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
+                    || !acc.getValue().equals( "NP_001025424" ) ) {
+                return false;
+            }
+            n.setName( "NM_001030253" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
+                    || !acc.getValue().equals( "NM_001030253" ) ) {
+                return false;
+            }
+            n.setName( "BCL2_HUMAN" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
+                    || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+            n.setName( "P10415" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
+                    || !acc.getValue().equals( "P10415" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+            n.setName( " P10415 " );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
+                    || !acc.getValue().equals( "P10415" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+            n.setName( "_P10415|" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
+                    || !acc.getValue().equals( "P10415" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+            n.setName( "AY695820" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+                    || !acc.getValue().equals( "AY695820" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+            n.setName( "_AY695820_" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+                    || !acc.getValue().equals( "AY695820" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+            n.setName( "AAA59452" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+                    || !acc.getValue().equals( "AAA59452" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+            n.setName( "_AAA59452_" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+                    || !acc.getValue().equals( "AAA59452" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+            n.setName( "AAA59452.1" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+                    || !acc.getValue().equals( "AAA59452.1" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+            n.setName( "_AAA59452.1_" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+                    || !acc.getValue().equals( "AAA59452.1" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+            n.setName( "GI:94894583" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
+                    || !acc.getValue().equals( "94894583" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            return false;
+        }
+        return true;
+    }
+
+    private static boolean testSequenceDbWsTools2() {
+        try {
+            final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
+            SequenceDbWsTools.obtainSeqInformation( n1 );
+            if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
+                return false;
+            }
+            if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
+                return false;
+            }
+            if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
+                return false;
+            }
+            if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
+                return false;
+            }
+            final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
+            SequenceDbWsTools.obtainSeqInformation( n2 );
+            System.out.println( n2.toString() );
+            if ( !n2.getNodeData().getSequence().getName()
+                    .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) {
+                return false;
+            }
+            if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
+                return false;
+            }
+            if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
+                return false;
+            }
+            if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
+                return false;
+            }
+            final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
+            SequenceDbWsTools.obtainSeqInformation( n3 );
+            System.out.println( "n=" + n3.toString() );
+            if ( !n3.getNodeData().getSequence().getName()
+                    .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
+                return false;
+            }
+            if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
+                return false;
+            }
+            if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
+                return false;
+            }
+            if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
+                return false;
+            }
+        }
+        catch ( final IOException e ) {
+            System.out.println();
+            System.out.println( "the following might be due to absence internet connection:" );
+            e.printStackTrace( System.out );
+            return true;
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace();
+            return false;
+        }
+        return true;
+    }
+
+    private static boolean testEbiEntryRetrieval() {
+        try {
+            final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" );
+            if ( !entry.getAccession().equals( "AAK41263" ) ) {
+                System.out.println( entry.getAccession() );
+                return false;
+            }
+            if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
+                System.out.println( entry.getTaxonomyScientificName() );
+                return false;
+            }
+            if ( !entry.getSequenceName()
+                    .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
+                System.out.println( entry.getSequenceName() );
+                return false;
+            }
+            // if ( !entry.getSequenceSymbol().equals( "" ) ) {
+            //     System.out.println( entry.getSequenceSymbol() );
+            //     return false;
+            // }
+            if ( !entry.getGeneName().equals( "treX-like" ) ) {
+                System.out.println( entry.getGeneName() );
+                return false;
+            }
+            if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
+                System.out.println( entry.getTaxonomyIdentifier() );
+                return false;
+            }
+            if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) {
+                System.out.println( entry.getAnnotations().first().getRefValue() );
+                return false;
+            }
+            if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) {
+                System.out.println( entry.getAnnotations().first().getRefSource() );
+                return false;
+            }
+            if ( entry.getCrossReferences().size() != 5 ) {
+                return false;
+            }
+            //
+            final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
+            if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
+                return false;
+            }
+            if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) {
+                System.out.println( entry1.getTaxonomyScientificName() );
+                return false;
+            }
+            if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) {
+                System.out.println( entry1.getSequenceName() );
+                return false;
+            }
+            if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) {
+                System.out.println( entry1.getTaxonomyIdentifier() );
+                return false;
+            }
+            if ( !entry1.getGeneName().equals( "BCL2" ) ) {
+                System.out.println( entry1.getGeneName() );
+                return false;
+            }
+            if ( entry1.getCrossReferences().size() != 6 ) {
+                return false;
+            }
+            //
+            final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
+            if ( !entry2.getAccession().equals( "NM_184234" ) ) {
+                return false;
+            }
+            if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
+                System.out.println( entry2.getTaxonomyScientificName() );
+                return false;
+            }
+            if ( !entry2.getSequenceName()
+                    .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
+                System.out.println( entry2.getSequenceName() );
+                return false;
+            }
+            if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) {
+                System.out.println( entry2.getTaxonomyIdentifier() );
+                return false;
+            }
+            if ( !entry2.getGeneName().equals( "RBM39" ) ) {
+                System.out.println( entry2.getGeneName() );
+                return false;
+            }
+            if ( entry2.getCrossReferences().size() != 3 ) {
+                return false;
+            }
+            //
+            final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
+            if ( !entry3.getAccession().equals( "HM043801" ) ) {
+                return false;
+            }
+            if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) {
+                System.out.println( entry3.getTaxonomyScientificName() );
+                return false;
+            }
+            if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) {
+                System.out.println( entry3.getSequenceName() );
+                return false;
+            }
+            if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) {
+                System.out.println( entry3.getTaxonomyIdentifier() );
+                return false;
+            }
+            if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) {
+                System.out.println( entry3.getSequenceSymbol() );
+                return false;
+            }
+            if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
+                return false;
+            }
+            if ( entry3.getCrossReferences().size() != 8 ) {
+                return false;
+            }
+            //
+            //
+            final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
+            if ( !entry4.getAccession().equals( "AAA36557" ) ) {
+                return false;
+            }
+            if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
+                System.out.println( entry4.getTaxonomyScientificName() );
+                return false;
+            }
+            if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) {
+                System.out.println( entry4.getSequenceName() );
+                return false;
+            }
+            if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) {
+                System.out.println( entry4.getTaxonomyIdentifier() );
+                return false;
+            }
+            if ( !entry4.getGeneName().equals( "ras" ) ) {
+                System.out.println( entry4.getGeneName() );
+                return false;
+            }
+            //            if ( !entry4.getChromosome().equals( "ras" ) ) {
+            //                System.out.println( entry4.getChromosome() );
+            //                return false;
+            //            }
+            //            if ( !entry4.getMap().equals( "ras" ) ) {
+            //                System.out.println( entry4.getMap() );
+            //                return false;
+            //            }
+            //
+            //TODO fails:
+            //            final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );
+            //            if ( !entry5.getAccession().equals( "HM043801" ) ) {
+            //                return false;
+            //            }
+        }
+        catch ( final IOException e ) {
+            System.out.println();
+            System.out.println( "the following might be due to absence internet connection:" );
+            e.printStackTrace( System.out );
+            return true;
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace();
+            return false;
+        }
+        return true;
+    }
+
     private static boolean testUniprotEntryRetrieval() {
         try {
             final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
@@ -10818,6 +11543,12 @@ public final class Test {
             if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
                 return false;
             }
+            if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) {
+                return false;
+            }
+            if ( !entry.getGeneName().equals( "GOT2" ) ) {
+                return false;
+            }
             if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
                 return false;
             }