X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=3efa3540f5a216bee1b3432b249861e31c520cd3;hb=fea4064e24c6cb362b0e033cf7047afd20f5f53f;hp=dba82fdb5207407d116431654cb9881aabc645f6;hpb=e572f0142daf64409db0461f15215288137603f8;p=jalview.git

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index dba82fd..3efa354 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -40,6 +40,9 @@ import java.util.Locale;
 import java.util.Set;
 import java.util.SortedSet;
 
+import javax.net.ssl.HttpsURLConnection;
+import javax.net.ssl.SSLContext;
+
 import org.forester.application.support_transfer;
 import org.forester.archaeopteryx.AptxUtil;
 import org.forester.archaeopteryx.TreePanelUtil;
@@ -147,7 +150,7 @@ public final class Test {
     private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
     private final static double  ZERO_DIFF                 = 1.0E-9;
 
-    public static boolean isEqual( final double a, final double b ) {
+    private static boolean isEqual( final double a, final double b ) {
         return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
     }
 
@@ -178,6 +181,7 @@ public final class Test {
             System.exit( -1 );
         }
         final long start_time = new Date().getTime();
+        
         System.out.print( "Basic node methods: " );
         if ( Test.testBasicNodeMethods() ) {
             System.out.println( "OK." );
@@ -968,8 +972,8 @@ public final class Test {
             }
         }
         if ( PERFORM_WEB_TREE_ACCESS ) {
-            System.out.print( "NHX parsing from URL: " );
-            if ( Test.testNHXparsingFromURL() ) {
+            System.out.print( "TreeBase acccess: " );
+            if ( Test.testTreeBaseReading() ) {
                 System.out.println( "OK." );
                 succeeded++;
             }
@@ -977,8 +981,8 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            System.out.print( "NHX parsing from URL 2: " );
-            if ( Test.testNHXparsingFromURL2() ) {
+            System.out.print( "ToL access: " );
+            if ( Test.testToLReading() ) {
                 System.out.println( "OK." );
                 succeeded++;
             }
@@ -986,8 +990,8 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            System.out.print( "phyloXML parsing from URL: " );
-            if ( Test.testPhyloXMLparsingFromURL() ) {
+            System.out.print( "NHX parsing from URL: " );
+            if ( Test.testNHXparsingFromURL() ) {
                 System.out.println( "OK." );
                 succeeded++;
             }
@@ -995,8 +999,8 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            System.out.print( "TreeBase acccess: " );
-            if ( Test.testTreeBaseReading() ) {
+            System.out.print( "NHX parsing from URL 2: " );
+            if ( Test.testNHXparsingFromURL2() ) {
                 System.out.println( "OK." );
                 succeeded++;
             }
@@ -1004,9 +1008,8 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            //
-            System.out.print( "ToL access: " );
-            if ( Test.testToLReading() ) {
+            System.out.print( "phyloXML parsing from URL: " );
+            if ( Test.testPhyloXMLparsingFromURL() ) {
                 System.out.println( "OK." );
                 succeeded++;
             }
@@ -1014,7 +1017,6 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            //
             System.out.print( "TreeFam access: " );
             if ( Test.testTreeFamReading() ) {
                 System.out.println( "OK." );
@@ -1024,8 +1026,6 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
-            //
-            //
             System.out.print( "Pfam tree access: " );
             if ( Test.testPfamTreeReading() ) {
                 System.out.println( "OK." );
@@ -1054,7 +1054,7 @@ public final class Test {
         }
     }
 
-    public static boolean testEngulfingOverlapRemoval() {
+    private static boolean testEngulfingOverlapRemoval() {
         try {
             final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
             final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
@@ -1153,7 +1153,7 @@ public final class Test {
         return true;
     }
 
-    public static final boolean testNHXparsingFromURL2() {
+    private static final boolean testNHXparsingFromURL2() {
         try {
             final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
             final Phylogeny phys[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
@@ -1220,7 +1220,7 @@ public final class Test {
         return true;
     }
 
-    public static final boolean testNHXparsingFromURL() {
+    private 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 );
@@ -1288,7 +1288,7 @@ public final class Test {
         return true;
     }
 
-    public static boolean testOverlapRemoval() {
+    private static boolean testOverlapRemoval() {
         try {
             final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
             final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
@@ -1442,49 +1442,61 @@ public final class Test {
         return true;
     }
 
-    public static final boolean testPfamTreeReading() {
+    private static final boolean testPfamTreeReading() {
         try {
             final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" );
             final NHXParser parser = new NHXParser();
             parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             parser.setReplaceUnderscores( false );
             parser.setGuessRootedness( true );
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] phys = factory.create( u.openStream(), parser );
+            final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser);
             if ( ( phys == null ) || ( phys.length != 1 ) ) {
                 return false;
             }
             if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
                 return false;
             }
+            final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u, parser);
+            if ( ( phys2 == null ) || ( phys2.length != 1 ) ) {
+                return false;
+            }
+            if ( phys2[ 0 ].getNumberOfExternalNodes() != phys[ 0 ].getNumberOfExternalNodes() ) {
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace();
+            return false;
         }
         return true;
     }
 
-    public static final boolean testPhyloXMLparsingFromURL() {
+    private 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() );
+            final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() );
+            
             if ( ( phys == null ) || ( phys.length != 2 ) ) {
                 return false;
             }
+            final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() );
+            
+            if ( ( phys2 == null ) || ( phys2.length != 2 ) ) {
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace();
+            return false;
         }
         return true;
     }
 
-    public static final boolean testToLReading() {
+    private static final boolean testToLReading() {
         try {
             final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" );
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() );
+            final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, new TolParser() );
             if ( ( phys == null ) || ( phys.length != 1 ) ) {
                 return false;
             }
@@ -1497,47 +1509,138 @@ public final class Test {
             if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) {
                 return false;
             }
+            //
+            final URL u2 = new URL( WebserviceUtil.TOL_URL_BASE + "17706" );
+            final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, new TolParser() );
+            if ( ( phys2 == null ) || ( phys2.length != 1 ) ) {
+                return false;
+            }
+            if ( !phys2[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "17706" ) ) {
+                return false;
+            }
+            if ( phys2[ 0 ].getNumberOfExternalNodes() < 5 ) {
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace();
+            return false;
         }
         return true;
     }
 
-    public static final boolean testTreeBaseReading() {
+    private static final boolean testTreeBaseReading() {
         try {
-            final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );
+            final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "72557?format=nexus" );  
             final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
             parser.setReplaceUnderscores( true );
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] phys = factory.create( u.openStream(), parser );
+            final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser );
             if ( ( phys == null ) || ( phys.length != 1 ) ) {
                 return false;
             }
+            final URL u_1 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2406?format=nexus" );  
+            final NexusPhylogeniesParser parser_1 = new NexusPhylogeniesParser();
+            final Phylogeny[] phys_1 = ForesterUtil.readPhylogeniesFromUrl( u_1, parser_1 );
+            if ( ( phys_1 == null ) || ( phys_1.length != 1 ) ) {
+                return false;
+            }
+            final URL u_2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "422?format=nexus" );  
+            final NexusPhylogeniesParser parser_2 = new NexusPhylogeniesParser();
+            final Phylogeny[] phys_2 = ForesterUtil.readPhylogeniesFromUrl( u_2, parser_2 );
+            if ( ( phys_2 == null ) || ( phys_2.length != 1 ) ) {
+                return false;
+            }
+            final URL u_3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2654?format=nexus" );  
+            final NexusPhylogeniesParser parser_3 = new NexusPhylogeniesParser();
+            final Phylogeny[] phys_3 = ForesterUtil.readPhylogeniesFromUrl( u_3, parser_3 );
+             if ( ( phys_3 == null ) || ( phys_3.length != 1 ) ) {
+                return false;
+            }
+            final URL u_4 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );  
+            final NexusPhylogeniesParser parser_4 = new NexusPhylogeniesParser();
+            final Phylogeny[] phys_4 = ForesterUtil.readPhylogeniesFromUrl( u_4, parser_4 );
+             if ( ( phys_4 == null ) || ( phys_4.length != 1 ) ) {
+                return false;
+            }
             final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" );
             final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser();
             parser2.setReplaceUnderscores( true );
-            final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 );
+            final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, parser2 );
             if ( ( phys2 == null ) || ( phys2.length != 9 ) ) {
                 return false;
             }
+            final URL u3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14909?format=nexus" );
+            final NexusPhylogeniesParser parser3 = new NexusPhylogeniesParser();
+            final Phylogeny[] phys3 = ForesterUtil.readPhylogeniesFromUrl( u3, parser3 );
+            if ( ( phys3 == null ) || ( phys3.length != 2 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys4 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14525?format=nexus" ),
+                    new NexusPhylogeniesParser() );
+            if ( ( phys4 == null ) || ( phys4.length != 1 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys5 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15632?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys5 == null ) || ( phys5.length != 1 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys6 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "10190?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys6 == null ) || ( phys6.length != 1 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys7 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "13246?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys7 == null ) || ( phys7.length != 2 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys8 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "11662?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys8 == null ) || ( phys8.length != 2 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys9 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "562?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys9 == null ) || ( phys9.length != 4 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys16424 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "16424?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys16424 == null ) || ( phys16424.length != 1 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys17878 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "17878?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys17878 == null ) || ( phys17878.length != 17 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys18804 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "18804?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys18804 == null ) || ( phys18804.length != 2 ) ) {
+                return false;
+            }
+            final Phylogeny[] phys346 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "346?format=nexus" ) ,
+                    new NexusPhylogeniesParser() );
+            if ( ( phys346 == null ) || ( phys346.length != 1 ) ) {
+                return false;
+            }
         }
         catch ( final Exception e ) {
             e.printStackTrace();
+            return false;
         }
         return true;
     }
 
-    public static final boolean testTreeFamReading() {
+    private static final boolean testTreeFamReading() {
         try {
             final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" );
             final NHXParser parser = new NHXParser();
             parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
             parser.setReplaceUnderscores( false );
             parser.setGuessRootedness( true );
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny[] phys = factory.create( u.openStream(), parser );
+            final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser );
             if ( ( phys == null ) || ( phys.length != 1 ) ) {
                 return false;
             }
@@ -1547,6 +1650,7 @@ public final class Test {
         }
         catch ( final Exception e ) {
             e.printStackTrace();
+            return false;
         }
         return true;
     }
@@ -4891,12 +4995,22 @@ public final class Test {
 
     private static boolean testFastaParser() {
         try {
-            if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
+            FileInputStream fis1 = new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" );
+            if ( !FastaParser.isLikelyFasta( fis1 ) ) {
+                fis1.close();
                 return false;
             }
-            if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
+            else {
+                fis1.close();
+            }
+            FileInputStream fis2 = new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" );
+            if ( FastaParser.isLikelyFasta( fis2 ) ) {
+                fis2.close();
                 return false;
             }
+            else {
+                fis2.close();
+            }
             final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
             if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
                 return false;
@@ -12914,4 +13028,6 @@ public final class Test {
         }
         return true;
     }
+    
+    
 }