X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FUrlTreeReader.java;h=e3c81f9c303d92e6a4fe7344893b4f80d812e674;hb=56cc12bcb9783e1bd16f57e12534434c31901879;hp=36c62651f07496f417b7f7e7606cf2c20bbef49e;hpb=54d8e3a926c3cf3477199c8b85aca478230e223c;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
index 36c6265..e3c81f9 100644
--- a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
+++ b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
@@ -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 {
@@ -65,13 +62,12 @@ public class UrlTreeReader implements Runnable {
     }
 
     synchronized void readPhylogeniesFromWebservice() {
-        final long start_time = new Date().getTime();
         URL url = null;
         Phylogeny[] trees = null;
         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
         final PhylogeniesWebserviceClient client = webservices_manager
                 .getAvailablePhylogeniesWebserviceClient( _webservice_client_index );
-        String identifier = JOptionPane.showInputDialog( _main_frame, client.getInstructions() + "\n(Reference: "
+        String identifier = JOptionPane.showInputDialog( _main_frame.getThisFrame(), client.getInstructions() + "\n(Reference: "
                 + client.getReference() + ")", client.getDescription(), JOptionPane.QUESTION_MESSAGE );
         if ( ( identifier != null ) && ( identifier.trim().length() > 0 ) ) {
             identifier = identifier.trim();
@@ -85,7 +81,7 @@ public class UrlTreeReader implements Runnable {
                     id = -1;
                 }
                 if ( id < 1 ) {
-                    JOptionPane.showMessageDialog( _main_frame,
+                    JOptionPane.showMessageDialog( _main_frame.getThisFrame(),
                                                    "Identifier is expected to be a number",
                                                    "Can not open URL",
                                                    JOptionPane.ERROR_MESSAGE );
@@ -132,7 +128,7 @@ public class UrlTreeReader implements Runnable {
                     case PFAM:
                         parser = new NHXParser();
                         ( ( NHXParser ) parser )
-                        .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+                                .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
@@ -154,26 +150,25 @@ 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,
+                JOptionPane.showMessageDialog( _main_frame.getThisFrame(),
                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
                                                "Malformed URL",
                                                JOptionPane.ERROR_MESSAGE );
             }
             catch ( final IOException e ) {
                 exception = true;
-                JOptionPane.showMessageDialog( _main_frame,
+                JOptionPane.showMessageDialog( _main_frame.getThisFrame(),
                                                "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,
+                JOptionPane.showMessageDialog( _main_frame.getThisFrame(),
                                                "Could not read from " + url + "\n" + e.getLocalizedMessage(),
                                                "Failed to read tree from " + client.getName() + " for " + identifier,
                                                JOptionPane.ERROR_MESSAGE );
@@ -181,7 +176,7 @@ public class UrlTreeReader implements Runnable {
             catch ( final Exception e ) {
                 exception = true;
                 e.printStackTrace();
-                JOptionPane.showMessageDialog( _main_frame,
+                JOptionPane.showMessageDialog( _main_frame.getThisFrame(),
                                                e.getLocalizedMessage(),
                                                "Unexpected Exception",
                                                JOptionPane.ERROR_MESSAGE );
@@ -206,7 +201,7 @@ public class UrlTreeReader implements Runnable {
                                 WebserviceUtil.processInstructions( client, phylogeny );
                             }
                             catch ( final PhyloXmlDataFormatException e ) {
-                                JOptionPane.showMessageDialog( _main_frame,
+                                JOptionPane.showMessageDialog( _main_frame.getThisFrame(),
                                                                "Error:\n" + e.getLocalizedMessage(),
                                                                "Error",
                                                                JOptionPane.ERROR_MESSAGE );
@@ -217,7 +212,7 @@ public class UrlTreeReader implements Runnable {
                                 PhylogenyMethods.transferNodeNameToField( phylogeny, client.getNodeField(), false );
                             }
                             catch ( final PhyloXmlDataFormatException e ) {
-                                JOptionPane.showMessageDialog( _main_frame,
+                                JOptionPane.showMessageDialog( _main_frame.getThisFrame(),
                                                                "Error:\n" + e.getLocalizedMessage(),
                                                                "Error",
                                                                JOptionPane.ERROR_MESSAGE );
@@ -245,23 +240,23 @@ public class UrlTreeReader implements Runnable {
                         }
                         _main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
                         AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
-                                                                                 .getControlPanel(), _main_frame.getConfiguration() );
+                                .getControlPanel(), _main_frame.getConfiguration() );
                         _main_frame.getMainPanel().getControlPanel().showWhole();
                     }
                 }
             }
             else if ( !exception ) {
                 JOptionPane.showMessageDialog( null, ForesterUtil.wordWrap( "Failed to read in tree(s) from [" + url
-                                                                            + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE );
+                        + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE );
             }
             _main_frame.getContentPane().repaint();
             if ( ( trees != null ) && ( trees.length > 0 ) ) {
                 try {
                     JOptionPane.showMessageDialog( null,
                                                    ForesterUtil.wordWrap( "Successfully read in " + trees.length
-                                                                          + " tree(s) from [" + url + "]", 80 ),
-                                                                          "Success",
-                                                                          JOptionPane.INFORMATION_MESSAGE );
+                                                           + " tree(s) from [" + url + "]", 80 ),
+                                                   "Success",
+                                                   JOptionPane.INFORMATION_MESSAGE );
                 }
                 catch ( final Exception e ) {
                     // Not important if this fails, do nothing.