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[jalview.git] / forester / java / src / org / forester / test / Test.java
diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index f714686..8e40249 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -344,6 +344,15 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
+        System.out.print( "Node construction and parsing of NHX (node level): " );
+        if ( Test.testNHXNodeParsing2() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
         System.out.print( "NHX parsing iterating: " );
         if ( Test.testNHParsingIter() ) {
             System.out.println( "OK." );
@@ -8907,6 +8916,34 @@ public final class Test {
                 System.out.println( p61.toNewHampshire() );
                 return false;
             }
+            final String s62 = "(1[&type=\"X\",size=123,subtree=(1,2);]:0.003,2[&type=\"(X,Y:3)\"]:0.004)[&type=\"(X,Y)\"]:0.0;";
+            final Phylogeny p62 = factory.create( s62, new NHXParser() )[ 0 ];
+            if ( !p62.toNewHampshire()
+                    .equals( "(1:0.003,2:0.004):0.0;" ) ) {
+                System.out.println( p62.toNewHampshire() );
+                return false;
+            }
+            final String s63 = "(1:0.003[&type=\"X\",size=123,subtree=(1,2);],2:0.004[&type=\"(X,Y:3)\"]):0.0[&type=\"(X,Y)\"];";
+            final Phylogeny p63 = factory.create( s63, new NHXParser() )[ 0 ];
+            if ( !p63.toNewHampshire()
+                    .equals( "(1:0.003,2:0.004):0.0;" ) ) {
+                System.out.println( p63.toNewHampshire() );
+                return false;
+            }
+            final String s64 = "((1,2):[95.5],3);";
+            final Phylogeny p64 = factory.create( s64, new NHXParser() )[ 0 ];
+            if ( !p64.toNewHampshireX()
+                    .equals( "((1,2)[&&NHX:B=95.5],3)" ) ) {
+                System.out.println( p64.toNewHampshireX() );
+                return false;
+            }
+            final String s65 = "((1:0.1,2:0.2):0.3[10.2],3);";
+            final Phylogeny p65 = factory.create( s65, new NHXParser() )[ 0 ];
+            if ( !p65.toNewHampshireX()
+                    .equals( "((1:0.1,2:0.2):0.3[&&NHX:B=10.2],3)" ) ) {
+                System.out.println( p65.toNewHampshireX() );
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );
@@ -9805,6 +9842,151 @@ public final class Test {
         return true;
     }
 
+    
+    private static boolean testNHXNodeParsing2() {
+        try {
+          
+            final PhylogenyNode n0_0 = PhylogenyNode
+                    .createInstanceFromNhxString( "n0:[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n0_0.getName().equals( "n0" ) ) {
+                return false;
+            }
+            if ( !isEqual( n0_0.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n0_1 = PhylogenyNode
+                    .createInstanceFromNhxString( "n0[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n0_1.getName().equals( "n0" ) ) {
+                return false;
+            }
+            if ( !isEqual( n0_1.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n0_2 = PhylogenyNode
+                    .createInstanceFromNhxString( "n0:1E-3[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n0_2.getName().equals( "n0" ) ) {
+                return false;
+            }
+            if ( !isEqual( n0_2.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n0_3 = PhylogenyNode
+                    .createInstanceFromNhxString( "n0:1E-3:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n0_3.getName().equals( "n0" ) ) {
+                return false;
+            }
+            if ( !isEqual( n0_3.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n0_4 = PhylogenyNode
+                    .createInstanceFromNhxString( "n0:0.001:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n0_4.getName().equals( "n0" ) ) {
+                return false;
+            }
+            if ( !isEqual( n0_4.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n1_0 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_0.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( n1_0.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+               return false;
+            }
+            final PhylogenyNode n1_1 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]:0.001", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_1.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( n1_1.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+               return false;
+            }
+            if ( !isEqual( n1_1.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n1_2 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:0.001[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_2.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( n1_2.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+               return false;
+            }
+            if ( !isEqual( n1_2.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            final PhylogenyNode n1_3 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[&boostrap=69,&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_3.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( n1_3.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+               return false;
+            }
+            if ( !isEqual( n1_3.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_3.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+                return false;
+            }
+            if ( !n1_3.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) {
+                return false;
+            }
+            final PhylogenyNode n1_4 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&bootstrap=69,&!colour=#FFFFFF]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_4.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( n1_4.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+               return false;
+            }
+            if ( !isEqual( n1_4.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_4.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+                return false;
+            }
+            if ( !n1_4.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) {
+                return false;
+            }
+            final PhylogenyNode n1_5 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[69.0]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_5.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_5.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_5.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+                return false;
+            }       
+            final PhylogenyNode n1_6 = PhylogenyNode
+                    .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+            if ( !n1_6.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+                return false;
+            }
+           
+            if ( !isEqual( n1_6.getDistanceToParent(), 0.001 ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getStandardDeviation(), 0.11 ) ) {
+                return false;
+            }
+            if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getValue(), 0.95 ) ) {
+                return false;
+            }
+            if ( !n1_6.getBranchData().getConfidence( 0 ).getType().equals( "posterior probability" ) ) {
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
     private static boolean testNHXParsing() {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();