X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=c1fe276676973d08f180c17f30df232d0bb9c61d;hb=ad75f8e44a6c2cdd69cb86f7fbf5fbef3ef9836d;hp=4b7c07e6d1b0dcd72ab01909a98a0c732fdd0a39;hpb=37c97b109c3a03f4640bce3855069f8ad8e17123;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 4b7c07e..c1fe276 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,24 +1,24 @@
 /*
- * 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 2.6)
+ * 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;
 
 import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -59,6 +59,7 @@ public class DBRefFetcher implements Runnable
   StringBuffer sbuffer = new StringBuffer();
 
   boolean running = false;
+
   /**
    * picr client instance
    */
@@ -72,39 +73,45 @@ public class DBRefFetcher implements Runnable
 
   SequenceFetcher sfetcher;
 
+  private SequenceI[] alseqs;
+
   public DBRefFetcher()
   {
   }
 
   /**
-   * Creates a new SequenceFeatureFetcher object and fetches from the
-   * currently selected set of databases.
+   * Creates a new SequenceFeatureFetcher object and fetches from the currently
+   * selected set of databases.
    * 
    * @param seqs
-   *                fetch references for these sequences
+   *          fetch references for these sequences
    * @param af
-   *                the parent alignframe for progress bar monitoring.
+   *          the parent alignframe for progress bar monitoring.
    */
   public DBRefFetcher(SequenceI[] seqs, AlignFrame af)
   {
     this(seqs, af, null);
   }
+
   /**
-   * Creates a new SequenceFeatureFetcher object and fetches from the
-   * currently selected set of databases.
+   * Creates a new SequenceFeatureFetcher object and fetches from the currently
+   * selected set of databases.
    * 
    * @param seqs
-   *                fetch references for these sequences
+   *          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
+   *          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;
+    alseqs = new SequenceI[seqs.length];
     SequenceI[] ds = new SequenceI[seqs.length];
     for (int i = 0; i < seqs.length; i++)
     {
+      alseqs[i] = seqs[i];
       if (seqs[i].getDatasetSequence() != null)
         ds[i] = seqs[i].getDatasetSequence();
       else
@@ -113,12 +120,14 @@ public class DBRefFetcher implements Runnable
     this.dataset = ds;
     // TODO Jalview 2.5 lots of this code should be in the gui package!
     sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
-    if (sources==null)
+    if (sources == null)
     {
       // 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();
+      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())
       {
@@ -126,12 +135,14 @@ public class DBRefFetcher implements Runnable
         selsources.addElement(src.getNickname());
       }
       int osel = 0;
-      for (int o=0;otherdb!=null && o<otherdb.length;o++)
+      for (int o = 0; otherdb != null && o < otherdb.length; o++)
       {
         if (!selsources.contains(otherdb[o]))
         {
           otherdb[o] = null;
-        } else {
+        }
+        else
+        {
           osel++;
         }
       }
@@ -144,45 +155,54 @@ public class DBRefFetcher implements Runnable
       {
         defdb = DBRefSource.PROTEINDBS;
       }
-      // append the selected sequence sources to the default dbs 
-      dbSources = new String[defdb.length+osel];
+      // 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++)
+      for (int o = 0, op = defdb.length; otherdb != null
+              && o < otherdb.length; o++)
       {
-        if (otherdb[o]!=null)
+        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
+    }
+    else
+    {
+      // we assume the caller knows what they're doing and ensured that all the
+      // db source names are valid
       dbSources = sources;
     }
   }
+
   /**
-   * retrieve all the das sequence sources and add them to the list of db sources to retrieve from 
+   * 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 = new String[] {};
+      dbSources = new String[]
+      {};
     }
     // append additional sources
-    String[] otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
-    if (otherdb!=null && otherdb.length>0)
+    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);
+      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
    * 
    * @param waitTillFinished
-   *                true to block until the fetcher has finished
+   *          true to block until the fetcher has finished
    */
   public void fetchDBRefs(boolean waitTillFinished)
   {
@@ -209,9 +229,9 @@ public class DBRefFetcher implements Runnable
    * could be either seq name or dbref id
    * 
    * @param seq
-   *                SequenceI
+   *          SequenceI
    * @param key
-   *                String
+   *          String
    */
   void addSeqId(SequenceI seq, String key)
   {
@@ -254,8 +274,13 @@ public class DBRefFetcher implements Runnable
     running = true;
     long startTime = System.currentTimeMillis();
     af.setProgressBar("Fetching db refs", startTime);
-    try {
-      picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator().getAccessionMapperPort(); 
+    try
+    {
+      if (Cache.getDefault("DBREFFETCH_USEPICR", false))
+      {
+        picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator()
+                .getAccessionMapperPort();
+      }
     } catch (Exception e)
     {
       System.err.println("Couldn't locate PICR service instance.\n");
@@ -304,10 +329,10 @@ public class DBRefFetcher implements Runnable
         {
           // Still queries to make for current seqIndex
           StringBuffer queryString = new StringBuffer("");
-          int numq=0,nqSize = (maxqlen > queries.size()) ? queries.size()
-                  : maxqlen;
-          
-          while (queries.size()>0 && numq < nqSize)
+          int numq = 0, nqSize = (maxqlen > queries.size()) ? queries
+                  .size() : maxqlen;
+
+          while (queries.size() > 0 && numq < nqSize)
           {
             String query = (String) queries.elementAt(0);
             if (dbsource.isValidReference(query))
@@ -326,7 +351,9 @@ public class DBRefFetcher implements Runnable
           {
             if (jalview.bin.Cache.log.isDebugEnabled())
             {
-              jalview.bin.Cache.log.debug("Querying "+dbsource.getDbName()+" with : '"+queryString.toString()+"'");
+              jalview.bin.Cache.log.debug("Querying "
+                      + dbsource.getDbName() + " with : '"
+                      + queryString.toString() + "'");
             }
             retrieved = dbsource.getSequenceRecords(queryString.toString());
           } catch (Exception ex)
@@ -353,14 +380,12 @@ public class DBRefFetcher implements Runnable
                     { dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT
             // });
             // check for existing dbrefs to use
-            if (uprefs != null && uprefs.length>0)
+            if (uprefs != null && uprefs.length > 0)
             {
               for (int j = 0; j < uprefs.length; j++)
               {
                 addSeqId(sequence, uprefs[j].getAccessionId());
-                queries
-                        .addElement(uprefs[j].getAccessionId()
-                                .toUpperCase());
+                queries.addElement(uprefs[j].getAccessionId().toUpperCase());
               }
             }
             else
@@ -372,25 +397,40 @@ public class DBRefFetcher implements Runnable
               {
                 String token = st.nextToken();
                 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 (picrClient != null)
+                {
+                  // resolve the string against PICR to recover valid IDs
+                  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)
+                if (presp != null && presp.length > 0)
                 {
-                  for (int id=0;id<presp.length; id++)
+                  for (int id = 0; id < presp.length; id++)
                   {
-                    // construct sequences from response if sequences are present, and do a transferReferences
+                    // construct sequences from response if sequences are
+                    // present, and do a transferReferences
                     // otherwise transfer non sequence x-references directly.
                   }
-                  System.out.println("Validated ID against PICR... (for what its worth):"+token);
+                  System.out
+                          .println("Validated ID against PICR... (for what its worth):"
+                                  + token);
                   addSeqId(sequence, token);
                   queries.addElement(token.toUpperCase());
-                } else {
-                  //if ()
-                  //System.out.println("Not querying source with token="+token+"\n");
+                }
+                else
+                {
+                  // if ()
+                  // System.out.println("Not querying source with token="+token+"\n");
                   addSeqId(sequence, token);
                   queries.addElement(token.toUpperCase());
                 }
@@ -404,11 +444,10 @@ public class DBRefFetcher implements Runnable
     } // all databases have been queries.
     if (sbuffer.length() > 0)
     {
-      output
-              .setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"
-                      + "altered, most likely the start/end residue will have been updated.\n"
-                      + "Save your alignment to maintain the updated id.\n\n"
-                      + sbuffer.toString());
+      output.setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"
+              + "altered, most likely the start/end residue will have been updated.\n"
+              + "Save your alignment to maintain the updated id.\n\n"
+              + sbuffer.toString());
       Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
       // The above is the dataset, we must now find out the index
       // of the viewed sequence
@@ -431,13 +470,15 @@ public class DBRefFetcher implements Runnable
           AlignmentI retrievedAl) // File
   // file)
   {
-
     if (retrievedAl == null || retrievedAl.getHeight() == 0)
     {
       return;
     }
-    SequenceI[] retrieved = recoverDbSequences(retrievedAl.getSequencesArray());
+    SequenceI[] retrieved = recoverDbSequences(retrievedAl
+            .getSequencesArray());
     SequenceI sequence = null;
+    boolean transferred = false;
+    StringBuffer messages = new StringBuffer();
 
     // Vector entries = new Uniprot().getUniprotEntries(file);
 
@@ -451,9 +492,16 @@ public class DBRefFetcher implements Runnable
       // taking into account all accessionIds and names in the file
       Vector sequenceMatches = new Vector();
       // look for corresponding accession ids
-      DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry
-              .getDBRef(), new String[]
-      { dbSource });
+      DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
+              entry.getDBRef(), new String[]
+              { dbSource });
+      if (entryRefs == null)
+      {
+        System.err
+                .println("Dud dbSource string ? no entryrefs selected for "
+                        + dbSource + " on " + entry.getName());
+        continue;
+      }
       for (int j = 0; j < entryRefs.length; j++)
       {
         String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();
@@ -530,11 +578,11 @@ public class DBRefFetcher implements Runnable
           absStart = nonGapped.indexOf(entrySeq);
           if (absStart == -1)
           { // verification failed.
-            sbuffer.append(sequence.getName()
+            messages.append(sequence.getName()
                     + " SEQUENCE NOT %100 MATCH \n");
             continue;
           }
-
+          transferred = true;
           sbuffer.append(sequence.getName() + " HAS " + absStart
                   + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");
           //
@@ -554,6 +602,7 @@ public class DBRefFetcher implements Runnable
         }
         else
         {
+          transferred = true;
           // update start and end of local sequence to place it in entry's
           // reference frame.
           // apply identity map map from whole of local sequence to matching
@@ -565,20 +614,24 @@ public class DBRefFetcher implements Runnable
           // absStart+sequence.getStart()+entrySeq.length()-1},
           // new int[] { entry.getStart(), entry.getEnd() }, 1, 1);
           // relocate local features for updated start
-          if (updateRefFrame && sequence.getSequenceFeatures() != null)
+          if (updateRefFrame)
           {
-            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 (sequence.getSequenceFeatures() != null)
             {
-              if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)
+              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++)
               {
-                // shift feature along by absstart
-                sf[sfi].setBegin(sf[sfi].getBegin() + startShift);
-                sf[sfi].setEnd(sf[sfi].getEnd() + startShift);
+                if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)
+                {
+                  // shift feature along by absstart
+                  sf[sfi].setBegin(sf[sfi].getBegin() + startShift);
+                  sf[sfi].setEnd(sf[sfi].getEnd() + startShift);
+                }
               }
             }
           }
@@ -595,39 +648,71 @@ public class DBRefFetcher implements Runnable
           // finally, update local sequence reference frame if we're allowed
           sequence.setStart(absStart);
           sequence.setEnd(absEnd);
+          // search for alignment sequences to update coordinate frame for
+          for (int alsq = 0; alsq < alseqs.length; alsq++)
+          {
+            if (alseqs[alsq].getDatasetSequence() == sequence)
+            {
+              String ngAlsq = AlignSeq.extractGaps("-. ",
+                      alseqs[alsq].getSequenceAsString()).toUpperCase();
+              int oldstrt = alseqs[alsq].getStart();
+              alseqs[alsq].setStart(sequence.getSequenceAsString()
+                      .toUpperCase().indexOf(ngAlsq)
+                      + sequence.getStart());
+              if (oldstrt != alseqs[alsq].getStart())
+              {
+                alseqs[alsq].setEnd(ngAlsq.length()
+                        + alseqs[alsq].getStart() - 1);
+              }
+            }
+          }
+          // TODO: search for all other references to this dataset sequence, and
+          // update start/end
+          // TODO: update all AlCodonMappings which involve this alignment
+          // sequence (e.g. Q30167 cdna translation from exon2 product (vamsas
+          // demo)
         }
         // 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 ?
+        // TODO: should we make a note of sequences that have received new DB
+        // ids, so we can query all enabled DAS servers for them ?
       }
     }
+    if (!transferred)
+    {
+      // report the ID/sequence mismatches
+      sbuffer.append(messages);
+    }
   }
 
   /**
    * loop thru and collect additional sequences in Map.
+   * 
    * @param sequencesArray
    * @return
    */
   private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
   {
     Vector nseq = new Vector();
-    for (int i=0;sequencesArray!=null && i<sequencesArray.length;i++)
+    for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
     {
       nseq.addElement(sequencesArray[i]);
       DBRefEntry dbr[] = sequencesArray[i].getDBRef();
       jalview.datamodel.Mapping map = null;
-      for (int r=0;(dbr!=null) && r<dbr.length; r++) {
-        if ((map=dbr[r].getMap())!=null)
+      for (int r = 0; (dbr != null) && r < dbr.length; r++)
+      {
+        if ((map = dbr[r].getMap()) != null)
         {
-          if (!nseq.contains(map.getTo()))
+          if (map.getTo() != null && !nseq.contains(map.getTo()))
           {
             nseq.addElement(map.getTo());
           }
         }
       }
     }
-    if (nseq.size()>0) {
+    if (nseq.size() > 0)
+    {
       sequencesArray = new SequenceI[nseq.size()];
       nseq.toArray(sequencesArray);
     }