in progress

[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 68777de..47516e4 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -501,7 +501,7 @@ public final class Test {
                 failed++;
             }
         }
-        ///////////////////////////////////////// System.exit( 0 );
+        /////////////////////System.exit( 0 );
         System.out.print( "UniProtKB id extraction: " );
         if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
             System.out.println( "OK." );
@@ -759,9 +759,6 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        
-        
-        
         System.out.print( "Tree copy: " );
         if ( Test.testTreeCopy() ) {
             System.out.println( "OK." );
@@ -771,12 +768,6 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        
-        
-        
-        
-        
-        
         System.out.print( "Basic tree methods: " );
         if ( Test.testBasicTreeMethods() ) {
             System.out.println( "OK." );
@@ -2782,35 +2773,34 @@ 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])";
+            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() ) ) {
+            if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
                 return false;
             }
-            if ( !t1.toNewHampshireX().equals( str_0 )) {
+            if ( !t1.toNewHampshireX().equals( str_0 ) ) {
                 return false;
             }
             t0.deleteSubtree( t0.getNode( "c" ), true );
             t0.deleteSubtree( t0.getNode( "a" ), true );
-            t0.deleteSubtree( t0.getNode( "e" ), true );
-            if ( !t0.toNewHampshireX().equals( "(b,d)[&&NHX:S=lizards]" )) {
+            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 )) {
+            if ( !t1.toNewHampshireX().equals( str_0 ) ) {
                 return false;
             }
-            t0.deleteSubtree( t0.getNode( "b" ), true );
+            t0.deleteSubtree( t0.getNode( "e" ), true );
+            t0.deleteSubtree( t0.getNode( "Bee" ), true );
             t0.deleteSubtree( t0.getNode( "d" ), true );
-            if ( !t1.toNewHampshireX().equals( str_0 )) {
+            if ( !t1.toNewHampshireX().equals( str_0 ) ) {
                 return false;
             }
-            
         }
         catch ( final Exception e ) {
             e.printStackTrace();
@@ -2818,7 +2808,6 @@ public final class Test {
         }
         return true;
     }
-    
 
     private static boolean testCreateBalancedPhylogeny() {
         try {
@@ -11514,14 +11503,15 @@ public final class Test {
                 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;
-            //            }
+            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 FIXME gi...
             //
             //TODO fails:
             //            final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );