JAL-1115 refactor base collection for Alignment from Vector to locally synchronized...

[jalview.git] / src / jalview / io / VamsasAppDatastore.java

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index fb6465c..93460e3 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -42,6 +42,7 @@ import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
+import java.util.List;
 import java.util.Vector;
 import java.util.jar.JarInputStream;
 import java.util.jar.JarOutputStream;
@@ -546,12 +547,7 @@ public class VamsasAppDatastore
             else
             {
               // first find the alignment sequence to associate this with.
-              SequenceI jvalsq = null;
-              Enumeration jval = av.getAlignment().getSequences()
-                      .elements();
-              while (jval.hasMoreElements())
-              {
-                jvalsq = (SequenceI) jval.nextElement();
+              for (SequenceI jvalsq:av.getAlignment().getSequences()) {
                 // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence)
                 // sref, aa[i]);
                 if (jvalsq.getDatasetSequence() == aa[i].sequenceRef)
@@ -884,7 +880,7 @@ public class VamsasAppDatastore
    * creates/syncs the jvalsq from the alignment sequence
    */
   private boolean syncFromAlignmentSequence(AlignmentSequence valseq,
-          char valGapchar, char gapChar, Vector dsseqs)
+          char valGapchar, char gapChar, List<SequenceI> dsseqs)
 
   {
     boolean modal = false;
@@ -1573,7 +1569,7 @@ public class VamsasAppDatastore
         // ///LOAD DATASET
         DataSet dataset = root.getDataSet(_ds);
         int i, iSize = dataset.getSequenceCount();
-        Vector dsseqs;
+        List<SequenceI> dsseqs;
         jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
         int jremain = 0;
         if (jdataset == null)
@@ -1620,8 +1616,8 @@ public class VamsasAppDatastore
           SequenceI[] seqs = new SequenceI[dsseqs.size()];
           for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
           {
-            seqs[i] = (SequenceI) dsseqs.elementAt(i);
-            dsseqs.setElementAt(null, i);
+            seqs[i] = dsseqs.get(i);
+            dsseqs.set(i, null);
           }
           jdataset = new jalview.datamodel.Alignment(seqs);
           Cache.log.debug("New vamsas dataset imported into jalview.");
@@ -1782,8 +1778,8 @@ public class VamsasAppDatastore
               SequenceI[] seqs = new SequenceI[dsseqs.size()];
               for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
               {
-                seqs[i] = (SequenceI) dsseqs.elementAt(i);
-                dsseqs.setElementAt(null, i);
+                seqs[i] = dsseqs.get(i);
+                dsseqs.set(i,null);
               }
               jal = new jalview.datamodel.Alignment(seqs);
               Cache.log.debug("New vamsas alignment imported into jalview "