X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=5400d4e83e8f69eb489c4b554bbddc01d858d1df;hb=faf6281b4ee692a989d0d625b1bb0d581cc0269c;hp=c2d7ad5957d50817d08d1e760f0ca0d51f64057f;hpb=08fbe7c3d40a4077ab519334952a079968c07cd1;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index c2d7ad5..5400d4e 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,37 +1,48 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * 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
+ * 
  * 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 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.
- *
+ * 
  * 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
  */
 package jalview.ws;
 
-import java.io.*;
-import java.util.*;
-
-import org.exolab.castor.mapping.*;
-import org.exolab.castor.xml.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
-import jalview.gui.*;
-import jalview.ws.dbsources.Uniprot;
-import jalview.ws.ebi.EBIFetchClient;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.Desktop;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.OOMWarning;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import org.biojava.dasobert.dasregistry.DasSource;
+
+import uk.ac.ebi.picr.model.UPEntry;
 
 /**
- * DOCUMENT ME!
+ * Implements a runnable for validating a sequence against external databases
+ * and then propagating references and features onto the sequence(s)
  * 
  * @author $author$
  * @version $Revision$
@@ -40,13 +51,17 @@ public class DBRefFetcher implements Runnable
 {
   SequenceI[] dataset;
 
-  AlignFrame af;
+  IProgressIndicator af;
 
   CutAndPasteTransfer output = new CutAndPasteTransfer();
 
   StringBuffer sbuffer = new StringBuffer();
 
   boolean running = false;
+  /**
+   * picr client instance
+   */
+  uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;
 
   // /This will be a collection of Vectors of sequenceI refs.
   // The key will be the seq name or accession id of the seq
@@ -61,7 +76,8 @@ public class DBRefFetcher implements Runnable
   }
 
   /**
-   * Creates a new SequenceFeatureFetcher object.
+   * Creates a new SequenceFeatureFetcher object and fetches from the
+   * currently selected set of databases.
    * 
    * @param seqs
    *                fetch references for these sequences
@@ -70,6 +86,20 @@ public class DBRefFetcher implements Runnable
    */
   public DBRefFetcher(SequenceI[] seqs, AlignFrame af)
   {
+    this(seqs, af, null);
+  }
+  /**
+   * Creates a new SequenceFeatureFetcher object and fetches from the
+   * currently selected set of databases.
+   * 
+   * @param seqs
+   *                fetch references for these sequences
+   * @param af
+   *                the parent alignframe for progress bar monitoring.
+   * @param sources array of database source strings to query references from
+   */
+  public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources)
+  {
     this.af = af;
     SequenceI[] ds = new SequenceI[seqs.length];
     for (int i = 0; i < seqs.length; i++)
@@ -80,18 +110,73 @@ public class DBRefFetcher implements Runnable
         ds[i] = seqs[i];
     }
     this.dataset = ds;
-    sfetcher = new SequenceFetcher();
-    // select appropriate databases based on alignFrame context.
-    if (af.getViewport().getAlignment().isNucleotide())
+    // TODO Jalview 2.5 lots of this code should be in the gui package!
+    sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
+    if (sources==null)
     {
-      dbSources = DBRefSource.DNACODINGDBS;
+      // af.featureSettings_actionPerformed(null);
+      String[] defdb=null,otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+      Vector selsources = new Vector(), dasselsrc= (af.featureSettings!=null) ? af.featureSettings.getSelectedSources()
+              : new jalview.gui.DasSourceBrowser().getSelectedSources();
+      Enumeration en = dasselsrc.elements();
+      while (en.hasMoreElements())
+      {
+        DasSource src = (DasSource) en.nextElement();
+        selsources.addElement(src.getNickname());
+      }
+      int osel = 0;
+      for (int o=0;otherdb!=null && o<otherdb.length;o++)
+      {
+        if (!selsources.contains(otherdb[o]))
+        {
+          otherdb[o] = null;
+        } else {
+          osel++;
+        }
+      }
+      // select appropriate databases based on alignFrame context.
+      if (af.getViewport().getAlignment().isNucleotide())
+      {
+        defdb = DBRefSource.DNACODINGDBS;
+      }
+      else
+      {
+        defdb = DBRefSource.PROTEINDBS;
+      }
+      // append the selected sequence sources to the default dbs 
+      dbSources = new String[defdb.length+osel];
+      System.arraycopy(defdb, 0, dbSources, 0, defdb.length);
+      for (int o=0,op=defdb.length; otherdb!=null && o<otherdb.length; o++)
+      {
+        if (otherdb[o]!=null)
+        {
+          dbSources[op++] = otherdb[o];
+        }
+      }
+    } else {
+      // we assume the caller knows what they're doing and ensured that all the db source names are valid
+      dbSources = sources;
     }
-    else
+  }
+  /**
+   * retrieve all the das sequence sources and add them to the list of db sources to retrieve from 
+   */
+  public void appendAllDasSources()
+  {
+    if (dbSources == null)
     {
-      dbSources = DBRefSource.PROTEINDBS;
+      dbSources = new String[] {};
+    }
+    // append additional sources
+    String[] otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+    if (otherdb!=null && otherdb.length>0)
+    {
+      String[] newsrc = new String[dbSources.length+otherdb.length];
+      System.arraycopy(dbSources, 0, newsrc,0,dbSources.length);
+      System.arraycopy(otherdb, 0, newsrc,dbSources.length, otherdb.length);
+      dbSources = newsrc;
     }
   }
-
   /**
    * start the fetcher thread
    * 
@@ -165,9 +250,16 @@ public class DBRefFetcher implements Runnable
     {
       throw new Error("Implementation error. Must initialise dbSources");
     }
+    running = true;
     long startTime = System.currentTimeMillis();
     af.setProgressBar("Fetching db refs", startTime);
-    running = true;
+    try {
+      picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator().getAccessionMapperPort(); 
+    } catch (Exception e)
+    {
+      System.err.println("Couldn't locate PICR service instance.\n");
+      e.printStackTrace();
+    }
     int db = 0;
     Vector sdataset = new Vector();
     for (int s = 0; s < dataset.length; s++)
@@ -192,6 +284,10 @@ public class DBRefFetcher implements Runnable
         maxqlen = ((Integer) dbsource.getDbSourceProperties().get(
                 DBRefSource.MULTIACC)).intValue();
       }
+      else
+      {
+        maxqlen = 1;
+      }
       // iterate through db for each remaining un-verified sequence
       SequenceI[] currSeqs = new SequenceI[sdataset.size()];
       sdataset.copyInto(currSeqs);// seqs that are to be validated against
@@ -207,31 +303,38 @@ public class DBRefFetcher implements Runnable
         {
           // Still queries to make for current seqIndex
           StringBuffer queryString = new StringBuffer("");
-          int nqSize = (maxqlen > queries.size()) ? queries.size()
+          int numq=0,nqSize = (maxqlen > queries.size()) ? queries.size()
                   : maxqlen;
-          for (int nq = 0, numq = 0; nq < nqSize; nq++)
+          
+          while (queries.size()>0 && numq < nqSize)
           {
-            String query = (String) queries.elementAt(nq);
+            String query = (String) queries.elementAt(0);
             if (dbsource.isValidReference(query))
             {
-              queryString.append((nq == 0) ? "" : dbsource
+              queryString.append((numq == 0) ? "" : dbsource
                       .getAccessionSeparator());
               queryString.append(query);
               numq++;
             }
-          }
-          for (int nq = 0; nq < nqSize; nq++)
-          {
+            // remove the extracted query string
             queries.removeElementAt(0);
           }
           // make the queries and process the response
           AlignmentI retrieved = null;
           try
           {
+            if (jalview.bin.Cache.log.isDebugEnabled())
+            {
+              jalview.bin.Cache.log.debug("Querying "+dbsource.getDbName()+" with : '"+queryString.toString()+"'");
+            }
             retrieved = dbsource.getSequenceRecords(queryString.toString());
           } catch (Exception ex)
           {
             ex.printStackTrace();
+          } catch (OutOfMemoryError err)
+          {
+            new OOMWarning("retrieving database references ("
+                    + queryString.toString() + ")", err);
           }
           if (retrieved != null)
           {
@@ -249,7 +352,7 @@ public class DBRefFetcher implements Runnable
                     { dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT
             // });
             // check for existing dbrefs to use
-            if (uprefs != null)
+            if (uprefs != null && uprefs.length>0)
             {
               for (int j = 0; j < uprefs.length; j++)
               {
@@ -267,8 +370,27 @@ public class DBRefFetcher implements Runnable
               while (st.hasMoreTokens())
               {
                 String token = st.nextToken();
-                addSeqId(sequence, token);
-                queries.addElement(token.toUpperCase());
+                UPEntry[] presp = null;
+                try {
+                  presp=picrClient.getUPIForAccession(token, null, picrClient.getMappedDatabaseNames(), null, true);
+                } catch (Exception e) {
+                  System.err.println("Exception with Picr for '"+token+"'\n");
+                  e.printStackTrace();
+                }
+                if (presp!=null && presp.length>0)
+                {
+                  for (int id=0;id<presp.length; id++)
+                  {
+                    // construct sequences from response if sequences are present, and do a transferReferences
+                    // otherwise transfer non sequence x-references directly.
+                  }
+                  addSeqId(sequence, token);
+                  queries.addElement(token.toUpperCase());
+                } else {
+                  System.out.println("Not querying source with token="+token+"\n");
+                  //addSeqId(sequence, token);
+                  //queries.addElement(token.toUpperCase());
+                }
               }
             }
           }
@@ -346,14 +468,15 @@ public class DBRefFetcher implements Runnable
           }
         }
       }
-      if (sequenceMatches.size()==0)
+      if (sequenceMatches.size() == 0)
       {
-        // failed to match directly on accessionId==query so just compare all sequences to entry
+        // failed to match directly on accessionId==query so just compare all
+        // sequences to entry
         Enumeration e = seqRefs.keys();
         while (e.hasMoreElements())
         {
           Vector sqs = (Vector) seqRefs.get(e.nextElement());
-          if (sqs!=null && sqs.size()>0)
+          if (sqs != null && sqs.size() > 0)
           {
             Enumeration sqe = sqs.elements();
             while (sqe.hasMoreElements())
@@ -383,9 +506,12 @@ public class DBRefFetcher implements Runnable
       for (int m = 0; m < sequenceMatches.size(); m++)
       {
         sequence = (SequenceI) sequenceMatches.elementAt(m);
-        // only update start and end positions and shift features if there are no existing references
-        // TODO: test for legacy where uniprot or EMBL refs exist but no mappings are made (but content matches retrieved set)
-        boolean updateRefFrame = sequence.getDBRef()==null || sequence.getDBRef().length==0;
+        // only update start and end positions and shift features if there are
+        // no existing references
+        // TODO: test for legacy where uniprot or EMBL refs exist but no
+        // mappings are made (but content matches retrieved set)
+        boolean updateRefFrame = sequence.getDBRef() == null
+                || sequence.getDBRef().length == 0;
         // verify sequence against the entry sequence
 
         String nonGapped = AlignSeq.extractGaps("-. ",
@@ -405,20 +531,23 @@ public class DBRefFetcher implements Runnable
                     + " SEQUENCE NOT %100 MATCH \n");
             continue;
           }
-          
+
           sbuffer.append(sequence.getName() + " HAS " + absStart
-                + " PREFIXED RESIDUES COMPARED TO " + dbSource+"\n");
+                  + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");
           //
-          //      + " - ANY SEQUENCE FEATURES"
-          //        + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
+          // + " - ANY SEQUENCE FEATURES"
+          // + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
           // absStart = 0;
           // create valid mapping between matching region of local sequence and
           // the mapped sequence
           mp = new Mapping(null, new int[]
-          { sequence.getStart()+absStart, sequence.getStart()+absStart+entrySeq.length()-1 }, new int[]
-          { entry.getStart(),
-              entry.getStart() + entrySeq.length() - 1 }, 1, 1);
-          updateRefFrame=false; // mapping is based on current start/end so don't modify start and end
+          { sequence.getStart() + absStart,
+              sequence.getStart() + absStart + entrySeq.length() - 1 },
+                  new int[]
+                  { entry.getStart(),
+                      entry.getStart() + entrySeq.length() - 1 }, 1, 1);
+          updateRefFrame = false; // mapping is based on current start/end so
+          // don't modify start and end
         }
         else
         {
@@ -438,13 +567,15 @@ public class DBRefFetcher implements Runnable
             SequenceFeature[] sf = sequence.getSequenceFeatures();
             int start = sequence.getStart();
             int end = sequence.getEnd();
+            int startShift = 1 - absStart - start; // how much the features are
+            // to be shifted by
             for (int sfi = 0; sfi < sf.length; sfi++)
             {
               if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)
               {
                 // shift feature along by absstart
-                sf[sfi].setBegin(sf[sfi].getBegin() + absStart);
-                sf[sfi].setEnd(sf[sfi].getEnd() + absStart);
+                sf[sfi].setBegin(sf[sfi].getBegin() + startShift);
+                sf[sfi].setEnd(sf[sfi].getEnd() + startShift);
               }
             }
           }
@@ -465,6 +596,7 @@ public class DBRefFetcher implements Runnable
         // and remove it from the rest
         // TODO: decide if we should remove annotated sequence from set
         sdataset.remove(sequence);
+        // TODO: should we make a note of sequences that have received new DB ids, so we can query all enabled DAS servers for them ?
       }
     }
   }