X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FUrlTreeReader.java;h=ce6f712bd35acdec1150ae7a94e458837769a522;hb=c0439ed8b088887ffea2faf11bc7897333287cb3;hp=f96864fb4fa9bff1c64ab8f176714fd4f8733b4f;hpb=e174d62534f7fc6f3de133d523a402a87735b27f;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
index f96864f..ce6f712 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;
 
@@ -29,7 +29,6 @@ import java.io.File;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.Date;
 
 import javax.swing.JOptionPane;
 
@@ -45,8 +44,6 @@ 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;
 import org.forester.util.ForesterUtil;
 
 public class UrlTreeReader implements Runnable {
@@ -59,8 +56,12 @@ public class UrlTreeReader implements Runnable {
         _webservice_client_index = webservice_client_index;
     }
 
+    @Override
+    public void run() {
+        readPhylogeniesFromWebservice();
+    }
+
     synchronized void readPhylogeniesFromWebservice() {
-        final long start_time = new Date().getTime();
         URL url = null;
         Phylogeny[] trees = null;
         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
@@ -88,6 +89,7 @@ public class UrlTreeReader implements Runnable {
                 }
                 identifier = id + "";
             }
+            boolean exception = false;
             try {
                 String url_str = client.getUrl();
                 url_str = url_str.replaceFirst( PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier );
@@ -101,34 +103,43 @@ public class UrlTreeReader implements Runnable {
                         parser = new NexusPhylogeniesParser();
                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
                         break;
+                    case TREEBASE_TREE:
+                        parser = new NexusPhylogeniesParser();
+                        ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
+                        ( ( NexusPhylogeniesParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
+                        break;
+                    case TREEBASE_STUDY:
+                        parser = new NexusPhylogeniesParser();
+                        ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
+                        ( ( NexusPhylogeniesParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
+                        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.AGGRESSIVE );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
                     case PFAM:
                         parser = new NHXParser();
                         ( ( NHXParser ) parser )
-                                .setTaxonomyExtraction( PhylogenyMethods.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( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
+                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
                     case PHYLOXML:
-                        parser = new PhyloXmlParser();
+                        parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
                         break;
                     default:
                         throw new IllegalArgumentException( "unknown format: " + client.getReturnFormat() );
@@ -139,28 +150,31 @@ public class UrlTreeReader implements Runnable {
                 else {
                     _main_frame.getMainPanel().setWaitCursor();
                 }
-                final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-                trees = factory.create( url.openStream(), parser );
+                trees = ForesterUtil.readPhylogeniesFromUrl( url, parser );
             }
             catch ( final MalformedURLException e ) {
+                exception = true;
                 JOptionPane.showMessageDialog( _main_frame,
                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
                                                "Malformed URL",
                                                JOptionPane.ERROR_MESSAGE );
             }
             catch ( final IOException e ) {
+                exception = true;
                 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 ) {
+                exception = true;
                 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 ) {
+                exception = true;
                 e.printStackTrace();
                 JOptionPane.showMessageDialog( _main_frame,
                                                e.getLocalizedMessage(),
@@ -182,11 +196,6 @@ public class UrlTreeReader implements Runnable {
                             phylogeny.setRerootable( false );
                             phylogeny.setRooted( true );
                         }
-                        if ( client.getName().equals( WebserviceUtil.PFAM_NAME ) ) {
-                            phylogeny.setRerootable( false );
-                            phylogeny.setRooted( true );
-                            PhylogenyMethods.transferInternalNodeNamesToConfidence( phylogeny );
-                        }
                         if ( client.getProcessingInstructions() != null ) {
                             try {
                                 WebserviceUtil.processInstructions( client, phylogeny );
@@ -236,12 +245,16 @@ public class UrlTreeReader implements Runnable {
                     }
                 }
             }
+            else if ( !exception ) {
+                JOptionPane.showMessageDialog( null, ForesterUtil.wordWrap( "Failed to read in tree(s) from [" + url
+                        + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE );
+            }
             _main_frame.getContentPane().repaint();
-            if ( ( ( trees != null ) && ( trees.length > 0 ) ) && ( ( new Date().getTime() - start_time ) > 20000 ) ) {
+            if ( ( trees != null ) && ( trees.length > 0 ) ) {
                 try {
                     JOptionPane.showMessageDialog( null,
                                                    ForesterUtil.wordWrap( "Successfully read in " + trees.length
-                                                           + " evolutionry tree(s) from [" + url + "]", 80 ),
+                                                           + " tree(s) from [" + url + "]", 80 ),
                                                    "Success",
                                                    JOptionPane.INFORMATION_MESSAGE );
                 }
@@ -254,9 +267,4 @@ public class UrlTreeReader implements Runnable {
         _main_frame.activateSaveAllIfNeeded();
         System.gc();
     }
-
-    @Override
-    public void run() {
-        readPhylogeniesFromWebservice();
-    }
 }