inprogress

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 09effc3..c56d068 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -35,6 +35,7 @@ import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.InputStream;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.net.URI;
@@ -649,13 +650,13 @@ public final class AptxUtil {
         System.out.println( "[" + applet_name + "] > " + message );
     }
 
-    final static Phylogeny[] readPhylogeniesFromUrl( final URL url,
-                                                     final boolean phyloxml_validate_against_xsd,
-                                                     final boolean replace_underscores,
-                                                     final boolean internal_numbers_are_confidences,
-                                                     final TAXONOMY_EXTRACTION taxonomy_extraction,
-                                                     final boolean midpoint_reroot ) throws FileNotFoundException,
-            IOException {
+    final public static Phylogeny[] readPhylogeniesFromUrl( final URL url,
+                                                            final boolean phyloxml_validate_against_xsd,
+                                                            final boolean replace_underscores,
+                                                            final boolean internal_numbers_are_confidences,
+                                                            final TAXONOMY_EXTRACTION taxonomy_extraction,
+                                                            final boolean midpoint_reroot )
+            throws FileNotFoundException, IOException {
         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
         final PhylogenyParser parser;
         boolean nhx_or_nexus = false;
@@ -679,7 +680,9 @@ public final class AptxUtil {
             }
         }
         AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
-        final Phylogeny[] phys = factory.create( url.openStream(), parser );
+        final InputStream i = url.openStream();
+        final Phylogeny[] phys = factory.create( i, parser );
+        i.close();
         if ( phys != null ) {
             if ( nhx_or_nexus && internal_numbers_are_confidences ) {
                 for( final Phylogeny phy : phys ) {

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 923c109..038f965 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -42,8 +42,8 @@ public final class Constants {
     public final static boolean __SYNTH_LF                                                    = false;                                                               // TODO remove me
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.988 SR";
-    final static String         PRG_DATE                                                      = "140416";
+    final static String         VERSION                                                       = "0.989 beta";
+    final static String         PRG_DATE                                                      = "140514";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Arial", "Helvetica",
             "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans"  };

diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
index 89b826a..449721d 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -105,7 +105,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
 
     @Override
     public String getName() {
-        return "NN/NHX Parser";
+        return "NH/NHX Parser";
     }
 
     public final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
@@ -587,7 +587,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
         return phy;
     }
 
-    public final static NHXParser createInstance( final Object nhx_source ) throws NHXFormatException, IOException {
+    private final static NHXParser createInstance( final Object nhx_source ) throws NHXFormatException, IOException {
         final NHXParser parser = new NHXParser();
         parser.setSource( nhx_source );
         return parser;

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 000e3fa..5864f61 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -41,6 +41,7 @@ import java.util.Set;
 import java.util.SortedSet;
 
 import org.forester.application.support_transfer;
+import org.forester.archaeopteryx.AptxUtil;
 import org.forester.archaeopteryx.TreePanelUtil;
 import org.forester.archaeopteryx.webservices.WebserviceUtil;
 import org.forester.development.DevelopmentTools;
@@ -189,7 +190,6 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        System.exit( 0 );
         System.out.print( "Basic node methods: " );
         if ( Test.testBasicNodeMethods() ) {
             System.out.println( "OK." );
@@ -971,6 +971,15 @@ public final class Test {
                 System.out.println( "failed." );
                 failed++;
             }
+            System.out.print( "NHX parsing from URL 2: " );
+            if ( Test.testNHXparsingFromURL2() ) {
+                System.out.println( "OK." );
+                succeeded++;
+            }
+            else {
+                System.out.println( "failed." );
+                failed++;
+            }
             System.out.print( "phyloXML parsing from URL: " );
             if ( Test.testPhyloXMLparsingFromURL() ) {
                 System.out.println( "OK." );
@@ -1138,6 +1147,72 @@ public final class Test {
         return true;
     }
 
+    public 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 ),
+                                                                      false,
+                                                                      false,
+                                                                      false,
+                                                                      TAXONOMY_EXTRACTION.NO,
+                                                                      false );
+            if ( ( phys == null ) || ( phys.length != 5 ) ) {
+                return false;
+            }
+            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[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
+                                                                       false,
+                                                                       false,
+                                                                       false,
+                                                                       TAXONOMY_EXTRACTION.NO,
+                                                                       false );
+            if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
+                return false;
+            }
+            if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+                System.out.println( phys2[ 0 ].toNewHampshire() );
+                return false;
+            }
+            if ( !phys2[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+                System.out.println( phys2[ 1 ].toNewHampshire() );
+                return false;
+            }
+            final Phylogeny phys3[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
+                    + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
+            if ( ( phys3 == null ) || ( phys3.length != 1 ) ) {
+                return false;
+            }
+            if ( !phys3[ 0 ]
+                    .toNewHampshire()
+                    .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
+                System.out.println( phys3[ 0 ].toNewHampshire() );
+                return false;
+            }
+            final Phylogeny phys4[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
+                    + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
+            if ( ( phys4 == null ) || ( phys4.length != 1 ) ) {
+                return false;
+            }
+            if ( !phys4[ 0 ]
+                    .toNewHampshire()
+                    .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
+                System.out.println( phys4[ 0 ].toNewHampshire() );
+                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";

diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index a98df7a..700d120 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -27,8 +27,8 @@ package org.forester.util;
 
 public final class ForesterConstants {
 
-    public final static String  FORESTER_VERSION            = "1.032";
-    public final static String  FORESTER_DATE               = "140416";
+    public final static String  FORESTER_VERSION            = "1.033";
+    public final static String  FORESTER_DATE               = "140514";
     public final static String  PHYLO_XML_VERSION           = "1.10";
     public final static String  PHYLO_XML_LOCATION          = "http://www.phyloxml.org";
     public final static String  PHYLO_XML_XSD               = "phyloxml.xsd";