X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FUrlTreeReader.java;h=ea4bca0f986bdf5abe4bb1e89fc500c1b0ee089e;hb=7aa2563168935732ea6d59a3f1c6cd8bf9a4ad61;hp=838ce620b51499b99608b47ebcbb8f2e20f861a6;hpb=5958d8c92c06f76da04a466ef7636e93a640b6a3;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
index 838ce62..ea4bca0 100644
--- a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
+++ b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.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;
 
@@ -39,6 +39,7 @@ import org.forester.archaeopteryx.webservices.WebservicesManager;
 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.phyloxml.PhyloXmlDataFormatException;
 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
 import org.forester.io.parsers.tol.TolParser;
 import org.forester.phylogeny.Phylogeny;
@@ -102,27 +103,25 @@ public class UrlTreeReader implements Runnable {
                         break;
                     case NH:
                         parser = new NHXParser();
-                        ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
+                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( true );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
                     case NH_EXTRACT_TAXONOMY:
                         parser = new NHXParser();
-                        ( ( NHXParser ) parser )
-                                .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
                     case PFAM:
                         parser = new NHXParser();
-                        ( ( NHXParser ) parser )
-                                .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
                     case NHX:
                         parser = new NHXParser();
-                        ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
+                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
@@ -187,10 +186,26 @@ public class UrlTreeReader implements Runnable {
                             PhylogenyMethods.transferInternalNodeNamesToConfidence( phylogeny );
                         }
                         if ( client.getProcessingInstructions() != null ) {
-                            WebserviceUtil.processInstructions( client, phylogeny );
+                            try {
+                                WebserviceUtil.processInstructions( client, phylogeny );
+                            }
+                            catch ( final PhyloXmlDataFormatException e ) {
+                                JOptionPane.showMessageDialog( _main_frame,
+                                                               "Error:\n" + e.getLocalizedMessage(),
+                                                               "Error",
+                                                               JOptionPane.ERROR_MESSAGE );
+                            }
                         }
                         if ( client.getNodeField() != null ) {
-                            PhylogenyMethods.transferNodeNameToField( phylogeny, client.getNodeField() );
+                            try {
+                                PhylogenyMethods.transferNodeNameToField( phylogeny, client.getNodeField(), false );
+                            }
+                            catch ( final PhyloXmlDataFormatException e ) {
+                                JOptionPane.showMessageDialog( _main_frame,
+                                                               "Error:\n" + e.getLocalizedMessage(),
+                                                               "Error",
+                                                               JOptionPane.ERROR_MESSAGE );
+                            }
                         }
                         phylogeny.setIdentifier( new Identifier( identifier, client.getName() ) );
                         _main_frame.getJMenuBar().remove( _main_frame.getHelpMenu() );