Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 3543204..b1c987e 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -394,18 +394,19 @@ public class DBRefFetcher implements Runnable
                   && (i < 50); seqIndex++, i++)
           {
             SequenceI sequence = dataset[seqIndex];
-            DBRefEntry[] uprefs = DBRefUtils
+            List<DBRefEntry> uprefs = DBRefUtils
                     .selectRefs(sequence.getDBRefs(), new String[]
                     { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
             // });
             // check for existing dbrefs to use
-            if (uprefs != null && uprefs.length > 0)
+            if (uprefs != null && uprefs.size() > 0)
             {
-              for (int j = 0; j < uprefs.length; j++)
+              for (int j = 0, n = uprefs.size(); j < n; j++)
               {
-                addSeqId(sequence, uprefs[j].getAccessionId());
+               DBRefEntry upref = uprefs.get(j);
+                addSeqId(sequence, upref.getAccessionId());
                 queries.addElement(
-                        uprefs[j].getAccessionId().toUpperCase());
+                        upref.getAccessionId().toUpperCase());
               }
             }
             else
@@ -532,7 +533,7 @@ public class DBRefFetcher implements Runnable
       // taking into account all accessionIds and names in the file
       Vector<SequenceI> sequenceMatches = new Vector<>();
       // look for corresponding accession ids
-      DBRefEntry[] entryRefs = DBRefUtils
+      List<DBRefEntry> entryRefs = DBRefUtils
               .selectRefs(retrievedSeq.getDBRefs(), new String[]
               { dbSource });
       if (entryRefs == null)
@@ -542,9 +543,10 @@ public class DBRefFetcher implements Runnable
                         + dbSource + " on " + retrievedSeq.getName());
         continue;
       }
-      for (int j = 0; j < entryRefs.length; j++)
+      for (int j = 0, n = entryRefs.size(); j < n; j++)
       {
-        String accessionId = entryRefs[j].getAccessionId();
+       DBRefEntry ref = entryRefs.get(j);
+        String accessionId = ref.getAccessionId();
         // match up on accessionId
         if (seqRefs.containsKey(accessionId.toUpperCase()))
         {
@@ -582,7 +584,7 @@ public class DBRefFetcher implements Runnable
       // could be useful to extend this so we try to find any 'significant'
       // information in common between two sequence objects.
       /*
-       * DBRefEntry[] entryRefs =
+       * List<DBRefEntry> entryRefs =
        * jalview.util.DBRefUtils.selectRefs(entry.getDBRef(), new String[] {
        * dbSource }); for (int j = 0; j < entry.getName().size(); j++) { String
        * name = entry.getName().elementAt(j).toString(); if
@@ -603,7 +605,7 @@ public class DBRefFetcher implements Runnable
         // TODO: test for legacy where uniprot or EMBL refs exist but no
         // mappings are made (but content matches retrieved set)
         boolean updateRefFrame = sequence.getDBRefs() == null
-                || sequence.getDBRefs().length == 0;
+                || sequence.getDBRefs().size() == 0;
         // TODO:
         // verify sequence against the entry sequence
 
@@ -669,7 +671,8 @@ public class DBRefFetcher implements Runnable
             int startShift = absStart - sequenceStart + 1;
             if (startShift != 0)
             {
-              modified |= sequence.getFeatures().shiftFeatures(startShift);
+              modified |= sequence.getFeatures().shiftFeatures(1,
+                      startShift);
             }
           }
         }
@@ -753,8 +756,6 @@ 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 ?
       }
     }
     return modified;
@@ -782,28 +783,33 @@ public class DBRefFetcher implements Runnable
    */
   private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
   {
-    Vector<SequenceI> nseq = new Vector<>();
-    for (int i = 0; sequencesArray != null
-            && i < sequencesArray.length; i++)
+       int n;
+       if (sequencesArray == null || (n = sequencesArray.length) == 0)
+         return sequencesArray;
+    ArrayList<SequenceI> nseq = new ArrayList<>();
+    for (int i = 0;i < n; i++)
     {
-      nseq.addElement(sequencesArray[i]);
-      DBRefEntry[] dbr = sequencesArray[i].getDBRefs();
+      nseq.add(sequencesArray[i]);
+      List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
       Mapping map = null;
-      for (int r = 0; (dbr != null) && r < dbr.length; r++)
+      if (dbr != null)
       {
-        if ((map = dbr[r].getMap()) != null)
+        for (int r = 0, rn = dbr.size(); r < rn; r++)
         {
-          if (map.getTo() != null && !nseq.contains(map.getTo()))
+          if ((map = dbr.get(r).getMap()) != null)
           {
-            nseq.addElement(map.getTo());
-          }
+            if (map.getTo() != null && !nseq.contains(map.getTo()))
+            {
+              nseq.add(map.getTo());
+            }
+          }  
         }
       }
     }
+    // BH 2019.01.25 question here if this is the right logic. Return the original if nothing found?
     if (nseq.size() > 0)
     {
-      sequencesArray = new SequenceI[nseq.size()];
-      nseq.toArray(sequencesArray);
+      return nseq.toArray(new SequenceI[nseq.size()]);
     }
     return sequencesArray;
   }