X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDasSequenceFeatureFetcher.java;h=30fe7253f1ee69f5490ce771217d0d0ac8d07b15;hb=3bd894ddb06a8d9a1efd29c1705235031174e391;hp=d3c20ba3c15ef8fe0800a52cd47a874f29800a6b;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index d3c20ba..30fe725 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.ws;
 
@@ -23,6 +22,9 @@ import java.util.*;
 
 import javax.swing.*;
 
+import org.biodas.jdas.client.SourcesClient;
+import org.biodas.jdas.schema.sources.SOURCE;
+import org.biodas.jdas.schema.sources.SOURCES;
 import org.biojava.dasobert.das.*;
 import org.biojava.dasobert.das2.*;
 import org.biojava.dasobert.das2.io.*;
@@ -80,9 +82,9 @@ public class DasSequenceFeatureFetcher
    * Creates a new SequenceFeatureFetcher object. Uses default
    * 
    * @param align
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param ap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public DasSequenceFeatureFetcher(SequenceI[] sequences,
           FeatureSettings fsettings, Vector selectedSources)
@@ -94,18 +96,20 @@ public class DasSequenceFeatureFetcher
           FeatureSettings fsettings, Vector ourselectedSources,
           boolean checkDbrefs, boolean promptFetchDbrefs)
   {
-    this.selectedSources = new Vector(); 
+    this.selectedSources = new Vector();
     Enumeration sources = ourselectedSources.elements();
     // filter both sequences and sources to eliminate duplicates
     while (sources.hasMoreElements())
     {
       Object src = sources.nextElement();
-      if (!selectedSources.contains(src)) { 
-        selectedSources.addElement(src); 
-      };
+      if (!selectedSources.contains(src))
+      {
+        selectedSources.addElement(src);
+      }
+      ;
     }
     Vector sqs = new Vector();
-    for (int i=0; i<oursequences.length; i++)
+    for (int i = 0; i < oursequences.length; i++)
     {
       if (!sqs.contains(oursequences[i]))
       {
@@ -113,7 +117,8 @@ public class DasSequenceFeatureFetcher
       }
     }
     sequences = new SequenceI[sqs.size()];
-    for (int i=0; i<sequences.length; i++) {
+    for (int i = 0; i < sequences.length; i++)
+    {
       sequences[i] = (SequenceI) sqs.elementAt(i);
     }
     if (fsettings != null)
@@ -212,32 +217,34 @@ public class DasSequenceFeatureFetcher
       af.setProgressBar("Fetching DAS Sequence Features", startTime);
     }
 
-
     if (selectedSources == null || selectedSources.size() == 0)
     {
-      try {
-        DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();
-      
-      String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
-              "uniprot");
-      StringTokenizer st = new StringTokenizer(active, "\t");
-      selectedSources = new Vector();
-      String token;
-      while (st.hasMoreTokens())
+      try
       {
-        token = st.nextToken();
-        for (int i = 0; i < sources.length; i++)
+        DasSource[] sources = new jalview.gui.DasSourceBrowser()
+                .getDASSource();
+
+        String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
+                "uniprot");
+        StringTokenizer st = new StringTokenizer(active, "\t");
+        selectedSources = new Vector();
+        String token;
+        while (st.hasMoreTokens())
         {
-          if (sources[i].getNickname().equals(token))
+          token = st.nextToken();
+          for (int i = 0; i < sources.length; i++)
           {
-            selectedSources.addElement(sources[i]);
-            break;
+            if (sources[i].getNickname().equals(token))
+            {
+              selectedSources.addElement(sources[i]);
+              break;
+            }
           }
         }
-      }
       } catch (Exception ex)
       {
-        debug("Exception whilst setting default feature sources from registry and local preferences.",ex);
+        debug("Exception whilst setting default feature sources from registry and local preferences.",
+                ex);
       }
     }
 
@@ -330,8 +337,9 @@ public class DasSequenceFeatureFetcher
   private void setGuiFetchComplete()
   {
 
-    if (af != null)
+    if (!cancelled && af != null)
     {
+      // only update the progress bar if we've completed the fetch normally
       af.setProgressBar("DAS Feature Fetching Complete", startTime);
     }
 
@@ -505,8 +513,8 @@ public class DasSequenceFeatureFetcher
           for (int i = 0; i < features.length; i++)
           {
             // standard DAS feature-> jalview sequence feature transformation
-            SequenceFeature f = newSequenceFeature(features[i], source
-                    .getNickname());
+            SequenceFeature f = newSequenceFeature(features[i],
+                    source.getNickname());
             if (!parseSeqFeature(seq, f, features[i], source))
             {
               if (dbref.getMap() != null && f.getBegin() > 0
@@ -609,8 +617,8 @@ public class DasSequenceFeatureFetcher
             for (int i = 0; i < features.length; i++)
             {
               // standard DAS feature-> jalview sequence feature transformation
-              SequenceFeature f = newSequenceFeature(features[i], source
-                      .getNickname());
+              SequenceFeature f = newSequenceFeature(features[i],
+                      source.getNickname());
               if (!parseSeqFeature(seq, f, features[i], source))
               {
                 // just add as a simple sequence feature
@@ -648,20 +656,20 @@ public class DasSequenceFeatureFetcher
    * simple sequence feature.
    * 
    * @param seq
-   *                the sequence to annotate
+   *          the sequence to annotate
    * @param f
-   *                the jalview sequence feature generated from the DAS feature
+   *          the jalview sequence feature generated from the DAS feature
    * @param map
-   *                the sequence feature attributes
+   *          the sequence feature attributes
    * @param source
-   *                the source that emitted the feature
+   *          the source that emitted the feature
    * @return true if feature was consumed as another kind of annotation.
    */
   protected boolean parseSeqFeature(SequenceI seq, SequenceFeature f,
           Map map, Das1Source source)
   {
     SequenceI mseq = seq;
-    while (seq.getDatasetSequence()!=null)
+    while (seq.getDatasetSequence() != null)
     {
       seq = seq.getDatasetSequence();
     }
@@ -671,14 +679,18 @@ public class DasSequenceFeatureFetcher
       if (type.equalsIgnoreCase("protein_name"))
       {
         // parse name onto the alignment sequence or the dataset sequence.
-        if (seq.getDescription()==null || seq.getDescription().trim().length() == 0)
+        if (seq.getDescription() == null
+                || seq.getDescription().trim().length() == 0)
         {
-          // could look at the note series to pick out the first long name, for the moment just use the whole description string 
+          // could look at the note series to pick out the first long name, for
+          // the moment just use the whole description string
           seq.setDescription(f.getDescription());
         }
-        if (mseq.getDescription()==null || mseq.getDescription().trim().length() == 0)
+        if (mseq.getDescription() == null
+                || mseq.getDescription().trim().length() == 0)
         {
-          // could look at the note series to pick out the first long name, for the moment just use the whole description string 
+          // could look at the note series to pick out the first long name, for
+          // the moment just use the whole description string
           mseq.setDescription(f.getDescription());
         }
         return true;
@@ -700,29 +712,36 @@ public class DasSequenceFeatureFetcher
           dbr.setAccessionId(st.nextToken());
         }
         seq.addDBRef(dbr);
-        
+
         if (f.links != null && f.links.size() > 0)
         {
           // feature is also appended to enable links to be seen.
           // TODO: consider extending dbrefs to have their own links ?
-          // TODO: new feature: extract dbref links from DAS servers and add the URL pattern to the list of DB name associated links in the user's preferences ?
-          // for the moment - just fix up the existing feature so it displays correctly.
+          // TODO: new feature: extract dbref links from DAS servers and add the
+          // URL pattern to the list of DB name associated links in the user's
+          // preferences ?
+          // for the moment - just fix up the existing feature so it displays
+          // correctly.
           // f.setType(dbr.getSource());
-          //f.setDescription();
+          // f.setDescription();
           f.setValue("linkonly", Boolean.TRUE);
-          //f.setDescription("");
+          // f.setDescription("");
           Vector newlinks = new Vector();
           Enumeration it = f.links.elements();
           while (it.hasMoreElements())
           {
             String elm;
-            UrlLink urllink = new UrlLink(elm = (String)it.nextElement());
-            if (urllink.isValid()) {
+            UrlLink urllink = new UrlLink(elm = (String) it.nextElement());
+            if (urllink.isValid())
+            {
               urllink.setLabel(f.getDescription());
               newlinks.addElement(urllink.toString());
-            } else {
-              // couldn't parse the link properly. Keep it anyway - just in case.
-              debug("couldn't parse link string - "+elm);
+            }
+            else
+            {
+              // couldn't parse the link properly. Keep it anyway - just in
+              // case.
+              debug("couldn't parse link string - " + elm);
               newlinks.addElement(elm);
             }
           }
@@ -788,8 +807,9 @@ public class DasSequenceFeatureFetcher
       {
       }
 
-      SequenceFeature f = new SequenceFeature((String) dasfeature
-              .get("TYPE"), desc, start, end, score, nickname);
+      SequenceFeature f = new SequenceFeature(
+              (String) dasfeature.get("TYPE"), desc, start, end, score,
+              nickname);
 
       if (dasfeature.containsKey("LINK"))
       {
@@ -823,7 +843,7 @@ public class DasSequenceFeatureFetcher
    * 
    * @return list of sources
    */
-  public static DasSource[] getDASSources()
+  public static SOURCE[] getDASSources()
   {
 
     String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
@@ -835,42 +855,25 @@ public class DasSequenceFeatureFetcher
    * query the given URL for DasSources.
    * 
    * @param registryURL
-   *                return sources from registryURL
+   *          return sources from registryURL
    */
-  public static DasSource[] getDASSources(String registryURL)
+  public static SOURCE[] getDASSources(String registryURL)
   {
-    DasSourceReaderImpl reader = new DasSourceReaderImpl();
-
+    
     try
     {
       URL url = new URL(registryURL);
+      org.biodas.jdas.client.SourcesClientInterface client = new SourcesClient();
+      
+      SOURCES sources = client.fetchData(registryURL);
 
-      DasSource[] sources = reader.readDasSource(url);
-
-      List das1sources = new ArrayList();
-      for (int i = 0; i < sources.length; i++)
-      {
-        DasSource ds = sources[i];
-        if (ds instanceof Das2Source)
-        {
-          Das2Source d2s = (Das2Source) ds;
-          if (d2s.hasDas1Capabilities())
-          {
-            Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
-            das1sources.add(d1s);
-          }
-
-        }
-        else if (ds instanceof Das1Source)
-        {
-          das1sources.add((Das1Source) ds);
-        }
-      }
+      List<SOURCE> dassources = sources.getSOURCE();
 
-      return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources
-              .size()]);
+      return dassources.toArray(new SOURCE[dassources.size()]);
     } catch (Exception ex)
     {
+      System.err.println("Failed to contact DAS1 registry at "
+              + registryURL);
       ex.printStackTrace();
       return null;
     }