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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 9326fd1..b1a9cd1 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -127,7 +127,7 @@ import org.forester.ws.wabi.TxSearch.TAX_RANK;
 @SuppressWarnings( "unused")
 public final class Test {
 
-    private final static boolean PERFORM_DB_TESTS          = true;
+    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"
@@ -490,18 +490,6 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        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." );
@@ -521,6 +509,18 @@ public final class Test {
             failed++;
         }
         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 );
+        if ( PERFORM_DB_TESTS ) {
             System.out.print( "Sequence DB tools 2: " );
             if ( testSequenceDbWsTools2() ) {
                 System.out.println( "OK." );
@@ -532,6 +532,7 @@ public final class Test {
                 System.exit( -1 );
             }
         }
+        // System.exit( 0 );
         System.out.print( "Hmmscan output parser: " );
         if ( testHmmscanOutputParser() ) {
             System.out.println( "OK." );
@@ -759,6 +760,15 @@ 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." );
@@ -1355,7 +1365,7 @@ public final class Test {
     private static boolean testBasicPhyloXMLparsing() {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhyloXmlParser xml_parser = new PhyloXmlParser();
+            final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
             final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
                                                               xml_parser );
             if ( xml_parser.getErrorCount() > 0 ) {
@@ -1548,7 +1558,7 @@ public final class Test {
     private static boolean testBasicPhyloXMLparsingRoundtrip() {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhyloXmlParser xml_parser = new PhyloXmlParser();
+            final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
             if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
                 xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
             }
@@ -1900,7 +1910,7 @@ public final class Test {
                 // Do nothing -- means were not running from jar.
             }
             if ( xml_parser == null ) {
-                xml_parser = new PhyloXmlParser();
+                xml_parser = PhyloXmlParser.createPhyloXmlParser();
                 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
                     xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
                 }
@@ -2765,6 +2775,41 @@ 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 );
@@ -8495,7 +8540,7 @@ public final class Test {
                 // Do nothing -- means were not running from jar.
             }
             if ( xml_parser == null ) {
-                xml_parser = new PhyloXmlParser();
+                xml_parser = PhyloXmlParser.createPhyloXmlParser();
                 if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
                     xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
                 }
@@ -11253,6 +11298,20 @@ public final class Test {
                 System.out.println( acc.toString() );
                 return false;
             }
+            n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
+                    || !acc.getValue().equals( "71845847" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
+            n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
+            acc = SequenceDbWsTools.obtainSeqAccession( n );
+            if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+                    || !acc.getValue().equals( "AAZ45343.1" ) ) {
+                System.out.println( acc.toString() );
+                return false;
+            }
         }
         catch ( final Exception e ) {
             return false;
@@ -11278,7 +11337,6 @@ public final class Test {
             }
             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;
@@ -11294,7 +11352,6 @@ public final class Test {
             }
             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;
@@ -11459,20 +11516,37 @@ 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" );
             //            if ( !entry5.getAccession().equals( "HM043801" ) ) {
             //                return false;
             //            }
+            final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" );
+            if ( !entry5.getAccession().equals( "AAZ45343" ) ) {
+                return false;
+            }
+            if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) {
+                System.out.println( entry5.getTaxonomyScientificName() );
+                return false;
+            }
+            if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) {
+                System.out.println( entry5.getSequenceName() );
+                return false;
+            }
+            if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) {
+                System.out.println( entry5.getTaxonomyIdentifier() );
+                return false;
+            }
         }
         catch ( final IOException e ) {
             System.out.println();