X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=c2dfc549b38b10317a3cae453db66a875bf4f554;hb=713d694ab9ab4e0701fd756af1ea2a892f96ade9;hp=1078656bd7ab1308f9819783c9bc82302df49b23;hpb=ebabb46561f996b5fcd59bd202defd7b189ea5b6;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 1078656..c2dfc54 100644
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -64,6 +64,9 @@ import javax.swing.text.MaskFormatter;
 
 import org.forester.analysis.TaxonomyDataManager;
 import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 import org.forester.io.parsers.tol.TolParser;
 import org.forester.io.parsers.util.ParserUtils;
@@ -791,24 +794,6 @@ public final class AptxUtil {
         return AVAILABLE_FONT_FAMILIES_SORTED;
     }
 
-    final static void inferCommonPartOfScientificNames( final Phylogeny tree ) {
-        boolean inferred = false;
-        for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
-            final PhylogenyNode n = it.next();
-            if ( !n.getNodeData().isHasTaxonomy() && !n.isExternal() ) {
-                final String sn = PhylogenyMethods.inferCommonPartOfScientificNameOfDescendants( n );
-                if ( !ForesterUtil.isEmpty( sn ) ) {
-                    n.getNodeData().setTaxonomy( new Taxonomy() );
-                    n.getNodeData().getTaxonomy().setScientificName( sn );
-                    inferred = true;
-                }
-            }
-        }
-        if ( inferred ) {
-            tree.setRerootable( false );
-        }
-    }
-
     final static boolean isHasAssignedEvent( final PhylogenyNode node ) {
         if ( !node.getNodeData().isHasEvent() ) {
             return false;
@@ -919,17 +904,41 @@ public final class AptxUtil {
         System.out.println( "[" + applet_name + "] > " + message );
     }
 
-    final static Phylogeny[] readPhylogeniesFromUrl( final URL url, final boolean phyloxml_validate_against_xsd )
+    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 )
             throws FileNotFoundException, IOException {
         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-        PhylogenyParser parser = null;
+        final PhylogenyParser parser;
+        boolean nhx_or_nexus = false;
         if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
             parser = new TolParser();
         }
         else {
             parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
+            if ( parser instanceof NHXParser ) {
+                nhx_or_nexus = true;
+                final NHXParser nhx = ( NHXParser ) parser;
+                nhx.setReplaceUnderscores( replace_underscores );
+                nhx.setIgnoreQuotes( false );
+                nhx.setTaxonomyExtraction( taxonomy_extraction );
+            }
+            else if ( parser instanceof NexusPhylogeniesParser ) {
+                nhx_or_nexus = true;
+                final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
+                nex.setReplaceUnderscores( replace_underscores );
+                nex.setIgnoreQuotes( false );
+            }
         }
-        return factory.create( url.openStream(), parser );
+        final Phylogeny[] phys = factory.create( url.openStream(), parser );
+        if ( nhx_or_nexus && internal_numbers_are_confidences ) {
+            for( final Phylogeny phy : phys ) {
+                PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
+            }
+        }
+        return phys;
     }
 
     final static void removeBranchColors( final Phylogeny phy ) {
@@ -938,30 +947,52 @@ public final class AptxUtil {
         }
     }
 
-    final static void unexpectedError( final Error err ) {
-        err.printStackTrace();
+    final static void unexpectedError( final Error e ) {
+        System.err.println();
+        e.printStackTrace( System.err );
+        System.err.println();
         final StringBuffer sb = new StringBuffer();
-        for( final StackTraceElement s : err.getStackTrace() ) {
+        for( final StackTraceElement s : e.getStackTrace() ) {
             sb.append( s + "\n" );
         }
         JOptionPane
                 .showMessageDialog( null,
                                     "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
-                                            + Constants.AUTHOR_EMAIL + " \nError: " + err + "\n" + sb,
+                                            + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
+                                            + sb,
                                     "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
                                     JOptionPane.ERROR_MESSAGE );
         System.exit( -1 );
     }
 
-    final static void unexpectedException( final Exception ex ) {
-        ex.printStackTrace();
+    final static void outOfMemoryError( final OutOfMemoryError e ) {
+        System.err.println();
+        System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
+        System.err.println();
+        e.printStackTrace();
+        System.err.println();
+        JOptionPane.showMessageDialog( null,
+                                       "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option"
+                                               + "\n\nError: " + e.getLocalizedMessage(),
+                                       "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
+                                       JOptionPane.ERROR_MESSAGE );
+        System.exit( -1 );
+    }
+
+    final static void unexpectedException( final Exception e ) {
+        System.err.println();
+        e.printStackTrace( System.err );
+        System.err.println();
         final StringBuffer sb = new StringBuffer();
-        for( final StackTraceElement s : ex.getStackTrace() ) {
+        for( final StackTraceElement s : e.getStackTrace() ) {
             sb.append( s + "\n" );
         }
-        JOptionPane.showMessageDialog( null, "An unexpected exception has occured. \nPlease contact: "
-                + Constants.AUTHOR_EMAIL + " \nException: " + ex + "\n" + sb, "Unexpected Exception ["
-                + Constants.PRG_NAME + Constants.VERSION + "]", JOptionPane.ERROR_MESSAGE );
+        JOptionPane.showMessageDialog( null,
+                                       "An unexpected exception has occured. \nPlease contact: "
+                                               + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
+                                               + "\n" + sb,
+                                       "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
+                                       JOptionPane.ERROR_MESSAGE );
     }
 
     final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,