X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FDasSequenceFeatureFetcher.java;h=33791ad773008352344294067f74eeb425336896;hb=ac5f3842d7230ae9761f2330b86e515efab29ee5;hp=305160eb9a579c9ac8d09e68eaca14bf959fde7e;hpb=f3581eb4882e66b7d66a9573be5103358196fd2d;p=jalview.git

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 305160e..33791ad 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, 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
@@ -18,29 +18,19 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
-
-import jalview.gui.*;
-
+import java.net.*;
 import java.util.*;
 
-import java.net.URL;
-
-import org.biojava.dasobert.das.FeatureThread;
-import org.biojava.dasobert.eventmodel.FeatureEvent;
-import org.biojava.dasobert.eventmodel.FeatureListener;
-import org.biojava.dasobert.dasregistry.DasSource;
-
-import org.biojava.dasobert.das2.io.DasSourceReaderImpl;
-import org.biojava.dasobert.dasregistry.Das1Source;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.biojava.dasobert.das2.Das2Source;
-import org.biojava.dasobert.das2.DasSourceConverter;
+import javax.swing.*;
 
+import org.biojava.dasobert.das.*;
+import org.biojava.dasobert.das2.*;
+import org.biojava.dasobert.das2.io.*;
+import org.biojava.dasobert.dasregistry.*;
+import org.biojava.dasobert.eventmodel.*;
 import jalview.bin.Cache;
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-
-import javax.swing.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
 
 /**
  * DOCUMENT ME!
@@ -52,8 +42,10 @@ public class DasSequenceFeatureFetcher
 {
   SequenceI[] sequences;
   AlignFrame af;
+  FeatureSettings fsettings;
   StringBuffer sbuffer = new StringBuffer();
   Vector selectedSources;
+  boolean cancelled = false;
 
   long startTime;
 
@@ -65,12 +57,13 @@ public class DasSequenceFeatureFetcher
    * @param ap DOCUMENT ME!
    */
   public DasSequenceFeatureFetcher(SequenceI[] sequences,
-                                   final AlignFrame af,
+                                   FeatureSettings fsettings,
                                    Vector selectedSources)
   {
     this.selectedSources = selectedSources;
     this.sequences = sequences;
-    this.af = af;
+    this.af = fsettings.af;
+    this.fsettings = fsettings;
 
     int uniprotCount = 0;
     for (int i = 0; i < selectedSources.size(); i++)
@@ -121,10 +114,14 @@ public class DasSequenceFeatureFetcher
         thread.start();
       }
       else
+      {
         startFetching();
     }
+    }
     else
+    {
       startFetching();
+    }
 
     }
 
@@ -145,6 +142,7 @@ public class DasSequenceFeatureFetcher
     */
    void startFetching()
    {
+     cancelled = false;
      startTime = System.currentTimeMillis();
      af.setProgressBar("Fetching DAS Sequence Features", startTime);
 
@@ -180,7 +178,9 @@ public class DasSequenceFeatureFetcher
 
        sourcesRemaining = selectedSources.size();
        //Now sending requests one at a time to each server
-       for (int sourceIndex = 0; sourceIndex < selectedSources.size();
+       for (int sourceIndex = 0;
+            sourceIndex < selectedSources.size()
+            && !cancelled;
             sourceIndex++)
        {
          DasSource dasSource = (DasSource) selectedSources.elementAt(
@@ -190,12 +190,20 @@ public class DasSequenceFeatureFetcher
        }
    }
 
+   public void cancel()
+   {
+     af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
+     cancelled = true;
+   }
+
    int sourcesRemaining=0;
    void responseComplete(DasSource dasSource, SequenceI seq)
    {
      if (seq != null)
      {
-       for (int seqIndex = 0; seqIndex < sequences.length-1; seqIndex++)
+       for (int seqIndex = 0;
+            seqIndex < sequences.length-1
+            && !cancelled; seqIndex++)
        {
          if (sequences[seqIndex] == seq)
          {
@@ -212,7 +220,11 @@ public class DasSequenceFeatureFetcher
        af.setProgressBar("DAS Feature Fetching Complete", startTime);
 
        if(af.featureSettings!=null)
+      {
          af.featureSettings.setTableData();
+      }
+
+       fsettings.complete();
      }
 
    }
@@ -225,12 +237,15 @@ public class DasSequenceFeatureFetcher
      int end = af.getViewport().getEndSeq();
      int index;
      for(index=start; index<end; index++)
-      if(seq == af.getViewport().getAlignment().getSequenceAt(index).getDatasetSequence())
        {
-         af.alignPanel.repaint();
+      if (seq ==
+          af.getViewport().getAlignment().getSequenceAt(index).getDatasetSequence())
+      {
+        af.alignPanel.paintAlignment(true);
          break;
        }
    }
+  }
 
 
   void nextSequence(DasSource dasSource, SequenceI seq)
@@ -239,36 +254,46 @@ public class DasSequenceFeatureFetcher
           new String[]
           {
         //  jalview.datamodel.DBRefSource.PDB,
-          jalview.datamodel.DBRefSource.UNIPROT
+          jalview.datamodel.DBRefSource.UNIPROT,
+        //  jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord sys sources
       });
+// TODO: minimal list of DAS queries to make by querying with untyped ID if distinct from any typed IDs
+
+      boolean dasCoordSysFound = false;
 
-        if (uprefs != null)
+      if (uprefs != null)
         {
-          // we know the id for this entry, so don't note its ID in the unknownSequences list
-         // for (int j = 0; j < uprefs.length; j++)
+          // do any of these ids match the source's coordinate system ?
+          for (int j = 0; j < uprefs.length; j++)
           {
-
-            // Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end
             DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
-           // if(cs.length>0)
-             // System.out.println("err "+
-            for (int l = 0; l < cs.length; l++)
+
+            for(int csIndex=0; csIndex<cs.length; csIndex++)
             {
-              if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].
-                  getName(), uprefs[0]))
+              if (cs.length > 0 && jalview.util.DBRefUtils
+                  .isDasCoordinateSystem(cs[csIndex].getName(), uprefs[j]))
               {
-
                 Cache.log.debug("Launched fetcher for coordinate system " +
-                                   cs[l].getName());
+                                cs[0].getName());
+                //  Will have to pass any mapping information to the fetcher
+                //- the start/end for the DBRefEntry may not be the same as the sequence's start/end
 
+                System.out.println(seq.getName() + " " + (seq.getDatasetSequence() == null)
+                                   + " " + dasSource.getUrl());
+
+                dasCoordSysFound = false;
                 createFeatureFetcher(seq,
                                      dasSource,
-                                     uprefs[0].getAccessionId());
+                                     uprefs[j]);
+                break; // only do this for one reference - assume same source will send same features for all IDs
               }
+              else
+                System.out.println("IGNORE " + cs[csIndex].getName());
             }
           }
         }
-        else
+
+        if(!dasCoordSysFound)
         {
           String id = null;
           // try and use the name as the sequence id
@@ -293,12 +318,89 @@ public class DasSequenceFeatureFetcher
 
    }
 
-  /**
-   * fetch and add das features to a sequence using the given source URL and Id to create a feature request
-   * @param seq
-   * @param SourceUrl
-   * @param id
-   */
+
+/**
+ * fetch and add das features to a sequence using the given source URL and compatible DbRef id.
+ * new features are mapped using the DbRef mapping to the local coordinate system.
+ * @param seq
+ * @param SourceUrl
+ * @param dbref
+ */
+  protected void createFeatureFetcher(final SequenceI seq, final DasSource dasSource,
+        final DBRefEntry dbref) {
+
+    //////////////
+    /// fetch DAS features
+    final Das1Source source = new Das1Source();
+    source.setUrl(dasSource.getUrl());
+    source.setNickname(dasSource.getNickname());
+    if (dbref==null || dbref.getAccessionId()==null || dbref.getAccessionId().length()<1)
+    {
+      return;
+    }
+    Cache.log.debug("new Das Feature Fetcher for " + dbref.getSource()+":"+dbref.getAccessionId() + " querying " +
+                    dasSource.getUrl());
+    FeatureThread fetcher = new FeatureThread(dbref.getAccessionId()
+                                                //  +  ":" + start + "," + end,
+                                                , source);
+
+      fetcher.addFeatureListener(new FeatureListener()
+      {
+        public void comeBackLater(FeatureEvent e)
+        {
+          responseComplete(dasSource, seq);
+          Cache.log.debug("das source " + e.getDasSource().getNickname() +
+                          " asked us to come back in " + e.getComeBackLater() +
+                          " secs.");
+        }
+
+        public void newFeatures(FeatureEvent e)
+        {
+
+          Das1Source ds = e.getDasSource();
+
+          Map[] features = e.getFeatures();
+          // add features to sequence
+          Cache.log.debug("das source " + ds.getUrl() + " returned " +
+                          features.length + " features");
+
+          if (features.length > 0)
+          {
+            for (int i = 0; i < features.length; i++)
+            {
+              SequenceFeature f = newSequenceFeature(features[i],
+                  source.getNickname());
+              if (dbref.getMap()!=null && f.getBegin()>0 && f.getEnd()>0) {
+                Cache.log.debug("mapping from "+f.getBegin()+" - "+f.getEnd());
+                SequenceFeature vf[] = dbref.getMap().locateFeature(f);
+                if (vf!=null) {
+                  for (int v=0;v<vf.length;v++)
+                  {
+                    Cache.log.debug("mapping to "+v+": "+vf[v].getBegin()+" - "+vf[v].getEnd());
+                    seq.addSequenceFeature(vf[v]);
+                  }
+                }
+              } else {
+                seq.addSequenceFeature(f);
+              }
+            }
+
+            featuresAdded(seq);
+          }
+          else
+          {
+          //  System.out.println("No features found for " + seq.getName()
+          //                     + " from: " + e.getDasSource().getNickname());
+          }
+          responseComplete(dasSource, seq);
+
+        }
+      }
+
+      );
+
+      fetcher.start();
+    }
   protected void createFeatureFetcher(final SequenceI seq,
                                       final DasSource dasSource,
                                       String id)
@@ -387,7 +489,9 @@ public class DasSequenceFeatureFetcher
        */
       String desc = new String();
       if (dasfeature.containsKey("NOTE"))
+      {
         desc += (String) dasfeature.get("NOTE");
+      }
 
       int start = 0, end = 0;
       float score = 0f;
@@ -442,7 +546,7 @@ public class DasSequenceFeatureFetcher
     DasSourceReaderImpl reader = new DasSourceReaderImpl();
 
     String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
-        "http://das.sanger.ac.uk/registry/das1/sources/"
+        DasSourceBrowser.DEFAULT_REGISTRY
         );
 
     try