From: jprocter <Jim Procter>
Date: Tue, 24 Feb 2009 17:27:33 +0000 (+0000)
Subject: bug fixes (infinite loop when fetcher given same sequence several times, race conditi... 
X-Git-Tag: Release_2_5~342
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=07f37fd11cf7cc2e6c04f7ad88cf7abfcbcea227;p=jalview.git

bug fixes (infinite loop when fetcher given same sequence several times, race conditions when fetching features immediatly after fetching sequences) and enhanced parsing of protein_name dbref types and URL link handling for features with no label.
---

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 56ca9ea..2448402 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -31,6 +31,7 @@ import org.biojava.dasobert.eventmodel.*;
 import jalview.bin.Cache;
 import jalview.datamodel.*;
 import jalview.gui.*;
+import jalview.util.UrlLink;
 
 /**
  * DOCUMENT ME!
@@ -89,12 +90,30 @@ public class DasSequenceFeatureFetcher
     this(sequences, fsettings, selectedSources, true, true);
   }
 
-  public DasSequenceFeatureFetcher(SequenceI[] sequences,
+  public DasSequenceFeatureFetcher(SequenceI[] oursequences,
           FeatureSettings fsettings, Vector selectedSources,
           boolean checkDbrefs, boolean promptFetchDbrefs)
   {
-    this.selectedSources = selectedSources;
-    this.sequences = sequences;
+    this.selectedSources = new Vector(); 
+    Enumeration sources = selectedSources.elements();
+    // filter both sequences and sources to eliminate duplicates
+    while (sources.hasMoreElements())
+    {
+      Object src = sources.nextElement();
+      if (this.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;
@@ -191,14 +210,16 @@ public class DasSequenceFeatureFetcher
       af.setProgressBar("Fetching DAS Sequence Features", startTime);
     }
 
-    DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();
 
     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");
-      Vector selectedSources = new Vector();
+      selectedSources = new Vector();
       String token;
       while (st.hasMoreTokens())
       {
@@ -212,6 +233,10 @@ public class DasSequenceFeatureFetcher
           }
         }
       }
+      } catch (Exception ex)
+      {
+        debug("Exception whilst setting default feature sources from registry and local preferences.",ex);
+      }
     }
 
     if (selectedSources == null || selectedSources.size() == 0)
@@ -616,37 +641,94 @@ 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
+   * 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)
+  protected boolean parseSeqFeature(SequenceI seq, SequenceFeature f,
+          Map map, Das1Source source)
   {
-    // check if source has biosapiens or other sequence ontology label
-    if (f.getType()!=null && (f.getType().equalsIgnoreCase("DBXREF")
-            || f.getType().equalsIgnoreCase("DBREF")))
+    SequenceI mseq = seq;
+    while (seq.getDatasetSequence()!=null)
     {
-      // try to parse the accession out
-      
-      DBRefEntry dbr = new DBRefEntry();
-      dbr.setVersion(source.getNickname());
-      StringTokenizer st = new StringTokenizer(f.getDescription(),":");
-      if (st.hasMoreTokens())
+      seq = seq.getDatasetSequence();
+    }
+    if (f.getType() != null)
+    {
+      String type = f.getType();
+      if (type.equalsIgnoreCase("protein_name"))
       {
-        dbr.setSource(st.nextToken());
+        // 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;
       }
-      if (st.hasMoreTokens())
+      // check if source has biosapiens or other sequence ontology label
+      if (type.equalsIgnoreCase("DBXREF") || type.equalsIgnoreCase("DBREF"))
       {
-        dbr.setAccessionId(st.nextToken());
+        // 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;
       }
-      seq.addDBRef(dbr);
-      return true;
     }
     return false;
   }
@@ -695,10 +777,11 @@ public class DasSequenceFeatureFetcher
       try
       {
         Object scr = dasfeature.get("SCORE");
-        if (scr!=null)
-          {score = (float) Double.parseDouble(scr.toString());
-          
-          }
+        if (scr != null)
+        {
+          score = (float) Double.parseDouble(scr.toString());
+
+        }
       } catch (Exception ex)
       {
       }