X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDasSequenceFeatureFetcher.java;h=ab02baf672889a24e6ae7f51f77f7cb5848793ca;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=ef48d9fc186dbecbedba1c75ec41d95c503985fa;hpb=db1e52b178b349f9b43ea05de525fc5350270d58;p=jalview.git

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index ef48d9f..ab02baf 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 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;
 
@@ -31,6 +30,7 @@ import org.biojava.dasobert.eventmodel.*;
 import jalview.bin.Cache;
 import jalview.datamodel.*;
 import jalview.gui.*;
+import jalview.util.UrlLink;
 
 /**
  * DOCUMENT ME!
@@ -79,9 +79,9 @@ 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)
@@ -89,17 +89,40 @@ public class DasSequenceFeatureFetcher
     this(sequences, fsettings, selectedSources, true, true);
   }
 
-  public DasSequenceFeatureFetcher(SequenceI[] sequences,
-          FeatureSettings fsettings, Vector selectedSources,
+  public DasSequenceFeatureFetcher(SequenceI[] oursequences,
+          FeatureSettings fsettings, Vector ourselectedSources,
           boolean checkDbrefs, boolean promptFetchDbrefs)
   {
-    this.selectedSources = selectedSources;
-    this.sequences = sequences;
+    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);
+      }
+      ;
+    }
+    Vector sqs = new Vector();
+    for (int i = 0; i < oursequences.length; i++)
+    {
+      if (!sqs.contains(oursequences[i]))
+      {
+        sqs.addElement(oursequences[i]);
+      }
+    }
+    sequences = new SequenceI[sqs.size()];
+    for (int i = 0; i < sequences.length; i++)
+    {
+      sequences[i] = (SequenceI) sqs.elementAt(i);
+    }
     if (fsettings != null)
     {
       this.fsettings = fsettings;
       this.af = fsettings.af;
-      af.getViewport().setShowSequenceFeatures(true);
+      af.setShowSeqFeatures(true);
     }
     int uniprotCount = 0;
     for (int i = 0; i < selectedSources.size(); i++)
@@ -191,26 +214,35 @@ public class DasSequenceFeatureFetcher
       af.setProgressBar("Fetching DAS Sequence Features", startTime);
     }
 
-    DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();
-
     if (selectedSources == null || selectedSources.size() == 0)
     {
-      String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
-              "uniprot");
-      StringTokenizer st = new StringTokenizer(active, "\t");
-      Vector 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);
       }
     }
 
@@ -303,8 +335,9 @@ 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);
     }
 
@@ -477,45 +510,48 @@ 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());
-            if (dbref.getMap() != null && f.getBegin() > 0
-                    && f.getEnd() > 0)
+            if (!parseSeqFeature(seq, f, features[i], source))
             {
-              debug("mapping from " + f.getBegin() + " - " + f.getEnd());
-              SequenceFeature vf[] = null;
-
-              try
-              {
-                vf = dbref.getMap().locateFeature(f);
-              } catch (Exception ex)
+              if (dbref.getMap() != null && f.getBegin() > 0
+                      && f.getEnd() > 0)
               {
-                Cache.log
-                        .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to help@jalview.org.");
-                Cache.log.info("Mapping feature from " + f.getBegin()
-                        + " to " + f.getEnd() + " in dbref "
-                        + dbref.getAccessionId() + " in "
-                        + dbref.getSource());
-                Cache.log.info("using das Source " + ds.getUrl());
-                Cache.log.info("Exception", ex);
-              }
+                debug("mapping from " + f.getBegin() + " - " + f.getEnd());
+                SequenceFeature vf[] = null;
 
-              if (vf != null)
-              {
-                for (int v = 0; v < vf.length; v++)
+                try
                 {
-                  debug("mapping to " + v + ": " + vf[v].getBegin() + " - "
-                          + vf[v].getEnd());
-                  seq.addSequenceFeature(vf[v]);
+                  vf = dbref.getMap().locateFeature(f);
+                } catch (Exception ex)
+                {
+                  Cache.log
+                          .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
+                  Cache.log.info("Mapping feature from " + f.getBegin()
+                          + " to " + f.getEnd() + " in dbref "
+                          + dbref.getAccessionId() + " in "
+                          + dbref.getSource());
+                  Cache.log.info("using das Source " + ds.getUrl());
+                  Cache.log.info("Exception", ex);
+                }
+
+                if (vf != null)
+                {
+                  for (int v = 0; v < vf.length; v++)
+                  {
+                    debug("mapping to " + v + ": " + vf[v].getBegin()
+                            + " - " + vf[v].getEnd());
+                    seq.addSequenceFeature(vf[v]);
+                  }
                 }
               }
-            }
-            else
-            {
-              seq.addSequenceFeature(f);
+              else
+              {
+                seq.addSequenceFeature(f);
+              }
             }
           }
-
           featuresAdded(seq);
         }
         else
@@ -578,10 +614,14 @@ 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());
-
-              seq.addSequenceFeature(f);
+              if (!parseSeqFeature(seq, f, features[i], source))
+              {
+                // just add as a simple sequence feature
+                seq.addSequenceFeature(f);
+              }
             }
 
             featuresAdded(seq);
@@ -609,6 +649,110 @@ public class DasSequenceFeatureFetcher
   }
 
   /**
+   * examine the given sequence feature to determine if it should actually be
+   * turned into sequence annotation or database cross references rather than a
+   * simple sequence feature.
+   * 
+   * @param seq
+   *          the sequence to annotate
+   * @param f
+   *          the jalview sequence feature generated from the DAS feature
+   * @param map
+   *          the sequence feature attributes
+   * @param source
+   *          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)
+    {
+      seq = seq.getDatasetSequence();
+    }
+    if (f.getType() != null)
+    {
+      String type = f.getType();
+      if (type.equalsIgnoreCase("protein_name"))
+      {
+        // parse name onto the alignment sequence or the dataset sequence.
+        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
+          seq.setDescription(f.getDescription());
+        }
+        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
+          mseq.setDescription(f.getDescription());
+        }
+        return true;
+      }
+      // check if source has biosapiens or other sequence ontology label
+      if (type.equalsIgnoreCase("DBXREF") || type.equalsIgnoreCase("DBREF"))
+      {
+        // try to parse the accession out
+
+        DBRefEntry dbr = new DBRefEntry();
+        dbr.setVersion(source.getNickname());
+        StringTokenizer st = new StringTokenizer(f.getDescription(), ":");
+        if (st.hasMoreTokens())
+        {
+          dbr.setSource(st.nextToken());
+        }
+        if (st.hasMoreTokens())
+        {
+          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.
+          // f.setType(dbr.getSource());
+          // f.setDescription();
+          f.setValue("linkonly", Boolean.TRUE);
+          // 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.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);
+              newlinks.addElement(elm);
+            }
+          }
+          f.links = newlinks;
+          seq.addSequenceFeature(f);
+        }
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
    * creates a jalview sequence feature from a das feature document
    * 
    * @param dasfeature
@@ -651,7 +795,12 @@ public class DasSequenceFeatureFetcher
       }
       try
       {
-        score = Integer.parseInt(dasfeature.get("SCORE").toString());
+        Object scr = dasfeature.get("SCORE");
+        if (scr != null)
+        {
+          score = (float) Double.parseDouble(scr.toString());
+
+        }
       } catch (Exception ex)
       {
       }
@@ -662,12 +811,14 @@ public class DasSequenceFeatureFetcher
       if (dasfeature.containsKey("LINK"))
       {
         // Do not put feature extent in link text for non-positional features
-        if (f.begin==0 && f.end==0)
-        {        f.addLink(f.getType()+"|"
-                + dasfeature.get("LINK"));
-        } else {
+        if (f.begin == 0 && f.end == 0)
+        {
+          f.addLink(f.getType() + "|" + dasfeature.get("LINK"));
+        }
+        else
+        {
           f.addLink(f.getType() + " " + f.begin + "_" + f.end + "|"
-                        + dasfeature.get("LINK"));
+                  + dasfeature.get("LINK"));
         }
       }
 
@@ -701,7 +852,7 @@ 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)
   {
@@ -737,6 +888,8 @@ public class DasSequenceFeatureFetcher
               .size()]);
     } catch (Exception ex)
     {
+      System.err.println("Failed to contact DAS1 registry at "
+              + registryURL);
       ex.printStackTrace();
       return null;
     }