in progress...

[jalview.git] / forester / java / src / org / forester / surfacing / TestSurfacing.java

diff --git a/forester/java/src/org/forester/surfacing/TestSurfacing.java b/forester/java/src/org/forester/surfacing/TestSurfacing.java
index 1ccaf70..72141d2 100644 (file)
--- a/forester/java/src/org/forester/surfacing/TestSurfacing.java
+++ b/forester/java/src/org/forester/surfacing/TestSurfacing.java
@@ -42,7 +42,6 @@ import org.forester.evoinference.matrix.character.CharacterStateMatrix;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
 import org.forester.io.parsers.HmmPfamOutputParser;
-import org.forester.io.parsers.nexus.PaupLogParser;
 import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
@@ -176,12 +175,7 @@ public class TestSurfacing {
             return false;
         }
         System.out.println( "OK." );
-        System.out.print( "  Paup log parser: " );
-        if ( !TestSurfacing.testPaupLogParser( test_dir ) ) {
-            System.out.println( "failed." );
-            return false;
-        }
-        System.out.println( "OK." );
+       
         System.out.print( "  Binary state matrix to gain loss matrix: " );
         if ( !TestSurfacing.testBinaryStateMatrixToGainLossMatrix( test_dir ) ) {
             System.out.println( "failed." );
@@ -1315,7 +1309,7 @@ public class TestSurfacing {
         final BinaryStates O = BinaryStates.ABSENT;
         try {
             final CharacterStateMatrix<BinaryStates> binary_states_matrix_0 = new BasicCharacterStateMatrix<BinaryStates>( 7,
-                                                                                                                           6 );
+                    6 );
             binary_states_matrix_0.setIdentifier( 0, "A" );
             binary_states_matrix_0.setIdentifier( 1, "B" );
             binary_states_matrix_0.setIdentifier( 2, "C" );
@@ -1821,7 +1815,7 @@ public class TestSurfacing {
             final GenomeWideCombinableDomains gwcd_1 = BasicGenomeWideCombinableDomains
                     .createInstance( list_1, false, new BasicSpecies( "1" ), DomainCombinationType.DIRECTED );
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
-                                                                                                                "B" ) ) ) {
+                    "B" ) ) ) {
                 return false;
             }
             if ( gwcd_1.toBinaryDomainCombinations()
@@ -1833,7 +1827,7 @@ public class TestSurfacing {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
-                                                                                                                "C" ) ) ) {
+                    "C" ) ) ) {
                 return false;
             }
             if ( gwcd_1.toBinaryDomainCombinations()
@@ -1841,27 +1835,27 @@ public class TestSurfacing {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "B",
-                                                                                                                "C" ) ) ) {
+                    "C" ) ) ) {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "C",
-                                                                                                                "X" ) ) ) {
+                    "X" ) ) ) {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "C",
-                                                                                                                "Y" ) ) ) {
+                    "Y" ) ) ) {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
-                                                                                                                "X" ) ) ) {
+                    "X" ) ) ) {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
-                                                                                                                "Y" ) ) ) {
+                    "Y" ) ) ) {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "Y",
-                                                                                                                "A" ) ) ) {
+                    "A" ) ) ) {
                 return false;
             }
             if ( gwcd_1.toBinaryDomainCombinations()
@@ -1873,19 +1867,19 @@ public class TestSurfacing {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "X",
-                                                                                                                "Y" ) ) ) {
+                    "Y" ) ) ) {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "Y",
-                                                                                                                "X" ) ) ) {
+                    "X" ) ) ) {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
-                                                                                                                "Y" ) ) ) {
+                    "Y" ) ) ) {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A",
-                                                                                                                "X" ) ) ) {
+                    "X" ) ) ) {
                 return false;
             }
             if ( gwcd_1.toBinaryDomainCombinations()
@@ -1893,19 +1887,19 @@ public class TestSurfacing {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "M",
-                                                                                                                "N" ) ) ) {
+                    "N" ) ) ) {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "N",
-                                                                                                                "M" ) ) ) {
+                    "M" ) ) ) {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "N",
-                                                                                                                "P" ) ) ) {
+                    "P" ) ) ) {
                 return false;
             }
             if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "M",
-                                                                                                                "P" ) ) ) {
+                    "P" ) ) ) {
                 return false;
             }
             if ( gwcd_1.toBinaryDomainCombinations()
@@ -1917,11 +1911,11 @@ public class TestSurfacing {
                 return false;
             }
             if ( gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "XX",
-                                                                                                               "YY" ) ) ) {
+                    "YY" ) ) ) {
                 return false;
             }
             if ( gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "YY",
-                                                                                                               "XX" ) ) ) {
+                    "XX" ) ) ) {
                 return false;
             }
             if ( gwcd_1.toBinaryDomainCombinations()
@@ -1941,7 +1935,7 @@ public class TestSurfacing {
             //            if ( matrix_bc.getState( 0, 0 ) != X ) {
             //                return false;
             //            }
-            //        
+            //
             //
             //            final BasicCharacterStateMatrix<BinaryStates> dm = new BasicCharacterStateMatrix<BinaryStates>( new BinaryStates[][] {
             //                    { X, X, X, X, X, X }, { X, X, X, X, X, X } } );
@@ -3226,23 +3220,23 @@ public class TestSurfacing {
                 return false;
             }
             if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "v",
-                                                                                                                 "u" ) ) ) {
+                    "u" ) ) ) {
                 return false;
             }
             if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
-                                                                                                                 "v" ) ) ) {
+                    "v" ) ) ) {
                 return false;
             }
             if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
-                                                                                                                 "x" ) ) ) {
+                    "x" ) ) ) {
                 return false;
             }
             if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
-                                                                                                                 "u" ) ) ) {
+                    "u" ) ) ) {
                 return false;
             }
             if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z",
-                                                                                                                 "y" ) ) ) {
+                    "y" ) ) ) {
                 return false;
             }
             calc_u.setAllowDomainsToBeIgnored( true );
@@ -3333,23 +3327,23 @@ public class TestSurfacing {
                 return false;
             }
             if ( calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "v",
-                                                                                                                "u" ) ) ) {
+                    "u" ) ) ) {
                 return false;
             }
             if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
-                                                                                                                 "v" ) ) ) {
+                    "v" ) ) ) {
                 return false;
             }
             if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
-                                                                                                                 "x" ) ) ) {
+                    "x" ) ) ) {
                 return false;
             }
             if ( calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w",
-                                                                                                                "u" ) ) ) {
+                    "u" ) ) ) {
                 return false;
             }
             if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z",
-                                                                                                                 "y" ) ) ) {
+                    "y" ) ) ) {
                 return false;
             }
             calc_u.setAllowDomainsToBeIgnored( false );
@@ -3431,7 +3425,7 @@ public class TestSurfacing {
                 return false;
             }
             if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z",
-                                                                                                                 "y" ) ) ) {
+                    "y" ) ) ) {
                 return false;
             }
             if ( !isEqual( calc_u.calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore(),
@@ -3476,7 +3470,7 @@ public class TestSurfacing {
     private static boolean testDomainCombinationCounting( final File test_dir ) {
         try {
             final HmmPfamOutputParser parser = new HmmPfamOutputParser( new File( test_dir
-                    + ForesterUtil.getFileSeparator() + "hmmpfam_output2" ), "human", "ls" );
+                                                                                  + ForesterUtil.getFileSeparator() + "hmmpfam_output2" ), "human", "ls" );
             parser.setEValueMaximum( 0.2 );
             parser.setIgnoreDufs( true );
             parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
@@ -4549,7 +4543,7 @@ public class TestSurfacing {
     private static boolean testHmmPfamOutputParser( final File test_dir ) {
         try {
             final HmmPfamOutputParser parser = new HmmPfamOutputParser( new File( test_dir
-                    + ForesterUtil.getFileSeparator() + "hmmpfam_output" ), "human", "ls" );
+                                                                                  + ForesterUtil.getFileSeparator() + "hmmpfam_output" ), "human", "ls" );
             parser.setEValueMaximum( 0.2 );
             parser.setIgnoreDufs( true );
             parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
@@ -4627,7 +4621,7 @@ public class TestSurfacing {
                 return false;
             }
             final HmmPfamOutputParser parser2 = new HmmPfamOutputParser( new File( test_dir
-                    + ForesterUtil.getFileSeparator() + "hmmpfam_output_short" ), "human", "ls" );
+                                                                                   + ForesterUtil.getFileSeparator() + "hmmpfam_output_short" ), "human", "ls" );
             parser2.setEValueMaximum( 0.2 );
             parser2.setIgnoreDufs( true );
             parser2.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
@@ -4718,7 +4712,7 @@ public class TestSurfacing {
     private static boolean testHmmPfamOutputParserWithFilter( final File test_dir ) {
         try {
             HmmPfamOutputParser parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator()
-                    + "hmmpfam_output3" ), "human", "ls" );
+                                                                            + "hmmpfam_output3" ), "human", "ls" );
             parser.setEValueMaximum( 0.2 );
             parser.setIgnoreDufs( true );
             parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
@@ -5432,73 +5426,5 @@ public class TestSurfacing {
         return true;
     }
 
-    private static boolean testPaupLogParser( final File test_dir ) {
-        try {
-            final PaupLogParser parser = new PaupLogParser();
-            parser.setSource( new File( test_dir + ForesterUtil.getFileSeparator() + "paup_log_test_1" ) );
-            final CharacterStateMatrix<BinaryStates> matrix = parser.parse();
-            if ( matrix.getNumberOfIdentifiers() != 8 ) {
-                return false;
-            }
-            if ( !matrix.getIdentifier( 0 ).equals( "MOUSE" ) ) {
-                return false;
-            }
-            if ( !matrix.getIdentifier( 1 ).equals( "NEMVE" ) ) {
-                return false;
-            }
-            if ( !matrix.getIdentifier( 2 ).equals( "MONBE" ) ) {
-                return false;
-            }
-            if ( !matrix.getIdentifier( 3 ).equals( "DICDI" ) ) {
-                return false;
-            }
-            if ( !matrix.getIdentifier( 4 ).equals( "ARATH" ) ) {
-                return false;
-            }
-            if ( !matrix.getIdentifier( 5 ).equals( "6" ) ) {
-                return false;
-            }
-            if ( !matrix.getIdentifier( 6 ).equals( "7" ) ) {
-                return false;
-            }
-            if ( !matrix.getIdentifier( 7 ).equals( "8" ) ) {
-                return false;
-            }
-            if ( matrix.getNumberOfCharacters() != ( 66 + 66 + 28 ) ) {
-                return false;
-            }
-            if ( matrix.getState( 0, 4 ) != BinaryStates.ABSENT ) {
-                return false;
-            }
-            if ( matrix.getState( 0, 5 ) != BinaryStates.PRESENT ) {
-                return false;
-            }
-            if ( matrix.getState( 1, 5 ) != BinaryStates.PRESENT ) {
-                return false;
-            }
-            if ( matrix.getState( 7, 154 ) != BinaryStates.ABSENT ) {
-                return false;
-            }
-            if ( matrix.getState( 7, 155 ) != BinaryStates.PRESENT ) {
-                return false;
-            }
-            if ( matrix.getState( 7, 156 ) != BinaryStates.PRESENT ) {
-                return false;
-            }
-            if ( matrix.getState( 7, 157 ) != BinaryStates.ABSENT ) {
-                return false;
-            }
-            if ( matrix.getState( 7, 158 ) != BinaryStates.PRESENT ) {
-                return false;
-            }
-            if ( matrix.getState( 7, 159 ) != BinaryStates.ABSENT ) {
-                return false;
-            }
-        }
-        catch ( final Exception e ) {
-            e.printStackTrace( System.out );
-            return false;
-        }
-        return true;
-    }
+   
 }