X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=ad8c0f090de983a099e69c82841db784e2a7790a;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=73d106a85fb60a9701d08bdc01ed3223fb05b24f;hpb=4ec235370b49c38ae7e7b3a46f92f926fc430bf1;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 73d106a..ad8c0f0 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,20 +1,19 @@
 /*
- * 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;
 
@@ -500,6 +499,13 @@ public class DBRefFetcher implements Runnable
       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();
@@ -612,24 +618,26 @@ 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) {
+          if (updateRefFrame)
+          {
             if (sequence.getSequenceFeatures() != null)
             {
-            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)
+              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);
+                }
               }
             }
-            }
           }
         }
 
@@ -645,21 +653,28 @@ public class DBRefFetcher implements Runnable
           sequence.setStart(absStart);
           sequence.setEnd(absEnd);
           // search for alignment sequences to update coordinate frame for
-          for (int alsq = 0; alsq<alseqs.length; alsq++)
+          for (int alsq = 0; alsq < alseqs.length; alsq++)
           {
-            if (alseqs[alsq].getDatasetSequence()==sequence)
+            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);
+              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)
+          // 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