X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FUrlTreeReader.java;h=7d88a317b13f8153935d87b7f9c698faf044928f;hb=d17f81782b4ce0a50c963ccb0394e0d2ae796ad0;hp=729d5696affecd175f03cb2daa0ba07bdcb087ef;hpb=ccf4c584032d16ed0ed8d0678f01305887724f96;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
index 729d569..7d88a31 100644
--- a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
+++ b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,13 +15,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // 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;
 
@@ -39,9 +39,11 @@ 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;
+import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.data.Identifier;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
@@ -101,27 +103,27 @@ public class UrlTreeReader implements Runnable {
                         break;
                     case NH:
                         parser = new NHXParser();
-                        ( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.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( ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                                .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
                     case PFAM:
                         parser = new NHXParser();
                         ( ( NHXParser ) parser )
-                                .setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                                .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
                     case NHX:
                         parser = new NHXParser();
-                        ( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
+                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
@@ -147,14 +149,16 @@ public class UrlTreeReader implements Runnable {
                                                JOptionPane.ERROR_MESSAGE );
             }
             catch ( final IOException e ) {
-                JOptionPane.showMessageDialog( _main_frame, "Could not read from " + url + "\n"
-                        + e.getLocalizedMessage(), "Failed to read tree from " + client.getName() + " for "
-                        + identifier, JOptionPane.ERROR_MESSAGE );
+                JOptionPane.showMessageDialog( _main_frame,
+                                               "Could not read from " + url + "\n" + e.getLocalizedMessage(),
+                                               "Failed to read tree from " + client.getName() + " for " + identifier,
+                                               JOptionPane.ERROR_MESSAGE );
             }
             catch ( final NumberFormatException e ) {
-                JOptionPane.showMessageDialog( _main_frame, "Could not read from " + url + "\n"
-                        + e.getLocalizedMessage(), "Failed to read tree from " + client.getName() + " for "
-                        + identifier, JOptionPane.ERROR_MESSAGE );
+                JOptionPane.showMessageDialog( _main_frame,
+                                               "Could not read from " + url + "\n" + e.getLocalizedMessage(),
+                                               "Failed to read tree from " + client.getName() + " for " + identifier,
+                                               JOptionPane.ERROR_MESSAGE );
             }
             catch ( final Exception e ) {
                 e.printStackTrace();
@@ -181,13 +185,29 @@ public class UrlTreeReader implements Runnable {
                         if ( client.getName().equals( WebserviceUtil.PFAM_NAME ) ) {
                             phylogeny.setRerootable( false );
                             phylogeny.setRooted( true );
-                            ForesterUtil.transferInternalNodeNamesToConfidence( phylogeny );
+                            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 ) {
-                            ForesterUtil.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() );
@@ -210,7 +230,7 @@ public class UrlTreeReader implements Runnable {
                             my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
                         }
                         _main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
-                        Util.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
+                        AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
                                 .getControlPanel(), _main_frame.getConfiguration() );
                         _main_frame.getMainPanel().getControlPanel().showWhole();
                     }