inprogress

diff --git a/forester/java/src/org/forester/application/decoratorX.java b/forester/java/src/org/forester/application/decoratorX.java
index a65f048..58a2b00 100644 (file)
--- a/forester/java/src/org/forester/application/decoratorX.java
+++ b/forester/java/src/org/forester/application/decoratorX.java
@@ -48,7 +48,7 @@ public class decoratorX {
                 System.exit( -1 );
             }
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhyloXmlParser xml_parser = new PhyloXmlParser();
+            final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
             final Phylogeny phy = factory.create( intree, xml_parser )[ 0 ];
             final BasicTable<String> t = BasicTableParser.parse( intable, '\t' );
             final PhylogenyNodeIterator it = phy.iteratorExternalForward();

diff --git a/forester/java/src/org/forester/application/dom_dup.java b/forester/java/src/org/forester/application/dom_dup.java
index 64b4640..e9cdba0 100644 (file)
--- a/forester/java/src/org/forester/application/dom_dup.java
+++ b/forester/java/src/org/forester/application/dom_dup.java
@@ -51,7 +51,7 @@ public class dom_dup {
             final File intree_file = cla.getFile( 2 );
             final File species_groups_file = cla.getFile( 1 );
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny phy = factory.create( intree_file, new PhyloXmlParser() )[ 0 ];
+            final Phylogeny phy = factory.create( intree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
             ForesterUtil.programMessage( PRG_NAME, "Pattern string: " + pattern_str );
             final Pattern pattern = Pattern.compile( pattern_str );
             ForesterUtil.programMessage( PRG_NAME, "Pattern is: " + pattern );

diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java
index b16b733..7e2d514 100644 (file)
--- a/forester/java/src/org/forester/application/gsdi.java
+++ b/forester/java/src/org/forester/application/gsdi.java
@@ -180,7 +180,7 @@ public final class gsdi {
         }
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
+            gene_tree = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
         }
         catch ( final IOException e ) {
             fatalError( "error",

diff --git a/forester/java/src/org/forester/application/subtree_feature_count.java b/forester/java/src/org/forester/application/subtree_feature_count.java
index c5fe6f7..57d4620 100644 (file)
--- a/forester/java/src/org/forester/application/subtree_feature_count.java
+++ b/forester/java/src/org/forester/application/subtree_feature_count.java
@@ -45,7 +45,7 @@ public class subtree_feature_count {
             final double depth = cla.getOptionValueAsDouble( DEPTH_OPTION );
             final File intree_file = cla.getFile( 0 );
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny phy = factory.create( intree_file, new PhyloXmlParser() )[ 0 ];
+            final Phylogeny phy = factory.create( intree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
             execute( phy, depth );
         }
         catch ( final Exception e ) {
@@ -56,7 +56,11 @@ public class subtree_feature_count {
 
     private static StringBuilder analyzeSubtree( final PhylogenyNode n, final double depth ) {
         final PhylogenyNode node = moveUp( n, depth );
-        for( final PhylogenyNode ext : node.getAllExternalDescendants() ) {
+        final List<PhylogenyNode> ext_descs = node.getAllExternalDescendants();
+        for( final PhylogenyNode ext : ext_descs ) {
+            if ( ext.getIndicator() != 0 ) {
+                throw new RuntimeException( "this should not have happened" );
+            }
             ext.setIndicator( ( byte ) 1 );
         }
         int xray = 0;
@@ -66,7 +70,7 @@ public class subtree_feature_count {
         PhylogenyNode first_node = null;
         PhylogenyNode last_node = null;
         int c = 0;
-        for( final PhylogenyNode ext : node.getAllExternalDescendants() ) {
+        for( final PhylogenyNode ext : ext_descs ) {
             if ( is_first ) {
                 first_node = ext;
                 is_first = false;

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 368499a..5d13def 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -1761,7 +1761,7 @@ public final class MainFrameApplication extends MainFrame {
             }
         }
         if ( xml_parser == null ) {
-            xml_parser = new PhyloXmlParser();
+            xml_parser = PhyloXmlParser.createPhyloXmlParser();
         }
         return xml_parser;
     }
@@ -2227,7 +2227,8 @@ public final class MainFrameApplication extends MainFrame {
         if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
             if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
                 try {
-                    final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
+                    final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
+                            .createPhyloXmlParserXsdValidating(), file );
                     t = trees[ 0 ];
                 }
                 catch ( final Exception e ) {
@@ -2248,7 +2249,8 @@ public final class MainFrameApplication extends MainFrame {
             // "*.*":
             else {
                 try {
-                    final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
+                    final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
+                            .createPhyloXmlParserXsdValidating(), file );
                     t = trees[ 0 ];
                 }
                 catch ( final Exception e ) {

diff --git a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
index 1fb4a59..184e35e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
+++ b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
@@ -132,7 +132,7 @@ public class UrlTreeReader implements Runnable {
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
                     case PHYLOXML:
-                        parser = new PhyloXmlParser();
+                        parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
                         break;
                     default:
                         throw new IllegalArgumentException( "unknown format: " + client.getReturnFormat() );

diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java
index 983048f..8ca07b9 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java
@@ -75,7 +75,7 @@ public class PhyloXmlParser implements PhylogenyParser {
     private StringBuffer         _error_messages;
     private StringBuffer         _warning_messages;
 
-    public PhyloXmlParser() {
+    private PhyloXmlParser() {
         init();
         reset();
     }
@@ -279,6 +279,11 @@ public class PhyloXmlParser implements PhylogenyParser {
         return xml_parser;
     }
 
+    public static PhyloXmlParser createPhyloXmlParser() {
+        final PhyloXmlParser xml_parser = new PhyloXmlParser();
+        return xml_parser;
+    }
+
     private class PhyloXmlParserErrorHandler extends DefaultHandler {
 
         @Override

diff --git a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
index 7931248..bbd9820 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
+++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
@@ -76,7 +76,7 @@ public final class ParserUtils {
         PhylogenyParser parser = null;
         final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
         if ( first_line.startsWith( "<" ) ) {
-            parser = new PhyloXmlParser();
+            parser = PhyloXmlParser.createPhyloXmlParser();
             if ( phyloxml_validate_against_xsd ) {
                 final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
                 final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
@@ -127,7 +127,7 @@ public final class ParserUtils {
         }
         else if ( filename_lc.endsWith( ".xml" ) || filename_lc.endsWith( ".px" ) || filename_lc.endsWith( "phyloxml" )
                 || filename_lc.endsWith( ".zip" ) ) {
-            parser = new PhyloXmlParser();
+            parser = PhyloXmlParser.createPhyloXmlParser();
             if ( phyloxml_validate_against_xsd ) {
                 final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
                 final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
@@ -168,7 +168,7 @@ public final class ParserUtils {
         if ( parser == null ) {
             final String first_line = ForesterUtil.getFirstLine( url ).trim().toLowerCase();
             if ( first_line.startsWith( "<" ) ) {
-                parser = new PhyloXmlParser();
+                parser = PhyloXmlParser.createPhyloXmlParser();
                 if ( phyloxml_validate_against_xsd ) {
                     final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
                     final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index ae43b31..fc210a5 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -1365,7 +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 ) {
@@ -1558,7 +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 );
             }
@@ -1910,7 +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 );
                 }
@@ -8540,7 +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 );
                 }