X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=0744fdd52638937ccc049f99a0d4f5bfe54d57ed;hb=30ea6e22e29814b611cf523d0b39b9e0197e63dc;hp=a4cf12a0a69d41685f26955b204956cc8cbab626;hpb=391381d661a230af98751dd6eba77bb2353c4d3e;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index a4cf12a..0744fdd 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -37,8 +37,6 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.net.URL;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -94,8 +92,6 @@ import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.sequence.Sequence;
 import org.forester.util.BasicDescriptiveStatistics;
@@ -786,8 +782,6 @@ public final class MainFrameApplication extends MainFrame {
         _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
         _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
         _file_jmenu.addSeparator();
-        _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
-        _file_jmenu.addSeparator();
         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
         _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
                 .getAvailablePhylogeniesWebserviceClients().size() ];
@@ -831,7 +825,6 @@ public final class MainFrameApplication extends MainFrame {
         customizeJMenuItem( _open_item );
         _open_item
                 .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
-        customizeJMenuItem( _open_url_item );
         for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
             customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
         }
@@ -941,7 +934,7 @@ public final class MainFrameApplication extends MainFrame {
                 .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
         _options_jmenu
-                .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Value Format Errors" ) );
+                .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
         //
         _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
         _options_jmenu
@@ -1157,87 +1150,6 @@ public final class MainFrameApplication extends MainFrame {
         System.exit( 0 );
     }
 
-    @Override
-    void readPhylogeniesFromURL() {
-        URL url = null;
-        Phylogeny[] phys = null;
-        final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
-        final String url_string = JOptionPane.showInputDialog( this,
-                                                               message,
-                                                               "Use URL/webservice to obtain a phylogeny",
-                                                               JOptionPane.QUESTION_MESSAGE );
-        boolean nhx_or_nexus = false;
-        if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
-            try {
-                url = new URL( url_string );
-                PhylogenyParser parser = null;
-                if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
-                    parser = new TolParser();
-                }
-                else {
-                    parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
-                            .isValidatePhyloXmlAgainstSchema() );
-                }
-                if ( parser instanceof NexusPhylogeniesParser ) {
-                    nhx_or_nexus = true;
-                }
-                else if ( parser instanceof NHXParser ) {
-                    nhx_or_nexus = true;
-                }
-                if ( _mainpanel.getCurrentTreePanel() != null ) {
-                    _mainpanel.getCurrentTreePanel().setWaitCursor();
-                }
-                else {
-                    _mainpanel.setWaitCursor();
-                }
-                final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-                phys = factory.create( url.openStream(), parser );
-            }
-            catch ( final MalformedURLException e ) {
-                JOptionPane.showMessageDialog( this,
-                                               "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
-                                               "Malformed URL",
-                                               JOptionPane.ERROR_MESSAGE );
-            }
-            catch ( final IOException e ) {
-                JOptionPane.showMessageDialog( this,
-                                               "Could not read from " + url + "\n"
-                                                       + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
-                                               "Failed to read URL",
-                                               JOptionPane.ERROR_MESSAGE );
-            }
-            catch ( final Exception e ) {
-                JOptionPane.showMessageDialog( this,
-                                               ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
-                                               "Unexpected Exception",
-                                               JOptionPane.ERROR_MESSAGE );
-            }
-            finally {
-                if ( _mainpanel.getCurrentTreePanel() != null ) {
-                    _mainpanel.getCurrentTreePanel().setArrowCursor();
-                }
-                else {
-                    _mainpanel.setArrowCursor();
-                }
-            }
-            if ( ( phys != null ) && ( phys.length > 0 ) ) {
-                if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
-                    for( final Phylogeny phy : phys ) {
-                        PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
-                    }
-                }
-                AptxUtil.addPhylogeniesToTabs( phys,
-                                               new File( url.getFile() ).getName(),
-                                               new File( url.getFile() ).toString(),
-                                               getConfiguration(),
-                                               getMainPanel() );
-                _mainpanel.getControlPanel().showWhole();
-            }
-        }
-        activateSaveAllIfNeeded();
-        System.gc();
-    }
-
     void setMsa( final Msa msa ) {
         _msa = msa;
     }
@@ -2189,7 +2101,7 @@ public final class MainFrameApplication extends MainFrame {
                         if ( nhx_or_nexus ) {
                             for( final Phylogeny phy : phys ) {
                                 if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
-                                    PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
+                                    PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
                                 }
                                 if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
                                     one_desc = true;