X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=80a20b6939784166e02f09d83f4806c4c098bb8e;hb=6479c35c4734850f517a6ef8de0fce500fdd6693;hp=ed1daa10831644a3dfe37c83ee094907b5dedfc9;hpb=e22f363c7273fc888ef911ad1f20d520a6bf030e;p=jalview.git

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index ed1daa1..80a20b6 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -912,13 +912,13 @@ public final class Test {
             path = "C:\\Program Files\\mafft-win\\mafft.bat";
         }
         else {
-            path = "/home/czmasek/bin/mafft";
-        }
-        if ( !MsaInferrer.isInstalled( path ) ) {
             path = "mafft";
-        }
-        if ( !MsaInferrer.isInstalled( path ) ) {
-            path = "/usr/local/bin/mafft";
+            if ( !MsaInferrer.isInstalled( path ) ) {
+                path = "/usr/bin/mafft";
+            }
+            if ( !MsaInferrer.isInstalled( path ) ) {
+                path = "/usr/local/bin/mafft";
+            }
         }
         if ( MsaInferrer.isInstalled( path ) ) {
             System.out.print( "MAFFT (external program): " );
@@ -958,6 +958,15 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
+        System.out.print( "phyloXML parsing from URL: " );
+        if ( Test.testPhyloXMLparsingFromURL() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
         System.out.println();
         final Runtime rt = java.lang.Runtime.getRuntime();
         final long free_memory = rt.freeMemory() / 1000000;
@@ -1075,24 +1084,44 @@ public final class Test {
         return true;
     }
 
+    public static final boolean testPhyloXMLparsingFromURL() {
+        try {
+            final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
+            final URL u = new URL( s );
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
+            if ( ( phys == null ) || ( phys.length != 2 ) ) {
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace();
+        }
+        return true;
+    }
+
     public static final boolean testNHXparsingFromURL() {
         try {
             final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
             final URL u = new URL( s );
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final Phylogeny[] phys = factory.create( u, new NHXParser() );
-            if ( ( phys == null ) || ( phys.length != 1 ) ) {
+            if ( ( phys == null ) || ( phys.length != 5 ) ) {
                 return false;
             }
-            if ( !phys[ 0 ].toNewHampshire().equals( "((a,b),c);" ) ) {
+            if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
                 System.out.println( phys[ 0 ].toNewHampshire() );
                 return false;
             }
+            if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+                System.out.println( phys[ 1 ].toNewHampshire() );
+                return false;
+            }
             final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() );
-            if ( ( phys2 == null ) || ( phys2.length != 1 ) ) {
+            if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
                 return false;
             }
-            if ( !phys2[ 0 ].toNewHampshire().equals( "((a,b),c);" ) ) {
+            if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
                 System.out.println( phys2[ 0 ].toNewHampshire() );
                 return false;
             }
@@ -1103,42 +1132,30 @@ public final class Test {
             if ( !p.hasNext() ) {
                 return false;
             }
-            if ( !p.next().toNewHampshire().equals( "((a,b),c);" ) ) {
+            if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
                 return false;
             }
-            if ( p.hasNext() ) {
-                return false;
-            }
-            if ( p.next() != null ) {
-                return false;
-            }
-            if ( p.hasNext() ) {
-                return false;
-            }
-            if ( p.next() != null ) {
+            if ( !p.hasNext() ) {
                 return false;
             }
             p.reset();
             if ( !p.hasNext() ) {
                 return false;
             }
-            if ( !p.next().toNewHampshire().equals( "((a,b),c);" ) ) {
-                return false;
-            }
-            if ( p.hasNext() ) {
+            if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
                 return false;
             }
-            if ( p.next() != null ) {
+            if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
                 return false;
             }
-            if ( p.hasNext() ) {
+            p.reset();
+            if ( !p.hasNext() ) {
                 return false;
             }
-            if ( p.next() != null ) {
+            if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
                 return false;
             }
-            p.reset();
-            if ( !p.hasNext() ) {
+            if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
                 return false;
             }
         }
@@ -5681,10 +5698,10 @@ public final class Test {
 
     private static boolean testMsaQualityMethod() {
         try {
-            final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
-            final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
-            final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
-            final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
+            final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
+            final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
+            final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
+            final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
             final List<Sequence> l = new ArrayList<Sequence>();
             l.add( s0 );
             l.add( s1 );
@@ -5703,6 +5720,15 @@ public final class Test {
             if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
                 return false;
             }
+            if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) {
+                return false;
+            }
+            if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) {
+                return false;
+            }
+            if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) {
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );