Merge branch 'develop' into feature/JAL-2759

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 4fffe6f..c7ec757 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -216,34 +216,6 @@ public class Jalview2XML
     }
   }
 
-  void clearSeqRefs()
-  {
-    if (_cleartables)
-    {
-      if (seqRefIds != null)
-      {
-        seqRefIds.clear();
-      }
-      if (seqsToIds != null)
-      {
-        seqsToIds.clear();
-      }
-      if (incompleteSeqs != null)
-      {
-        incompleteSeqs.clear();
-      }
-      // seqRefIds = null;
-      // seqsToIds = null;
-    }
-    else
-    {
-      // do nothing
-      warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
-      // seqRefIds = new Hashtable();
-      // seqsToIds = new IdentityHashMap();
-    }
-  }
-
   void initSeqRefs()
   {
     if (seqsToIds == null)
@@ -1417,9 +1389,10 @@ public class Jalview2XML
         }
         else
         {
-          ArrayList<int[]> hiddenRegions = hidden.getHiddenColumnsCopy();
-          for (int[] region : hiddenRegions)
+          Iterator<int[]> hiddenRegions = hidden.iterator();
+          while (hiddenRegions.hasNext())
           {
+            int[] region = hiddenRegions.next();
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
             hc.setEnd(region[1]);
@@ -2295,6 +2268,7 @@ public class Jalview2XML
 
       jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
       af = loadJalviewAlign(jprovider);
+      af.setMenusForViewport();
 
     } catch (MalformedURLException e)
     {
@@ -4249,7 +4223,8 @@ public class Jalview2XML
       StructureData filedat = oldFiles.get(id);
       String pdbFile = filedat.getFilePath();
       SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
-      binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
+      binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
+              null);
       binding.addSequenceForStructFile(pdbFile, seq);
     }
     // and add the AlignmentPanel's reference to the view panel
@@ -5341,28 +5316,25 @@ public class Jalview2XML
 
   }
 
-  public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
-          boolean keepSeqRefs)
+  /**
+   * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
+   * view as XML (but not to file), and then reloading it
+   * 
+   * @param ap
+   * @return
+   */
+  public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
   {
     initSeqRefs();
     JalviewModel jm = saveState(ap, null, null, null);
 
-    if (!keepSeqRefs)
-    {
-      clearSeqRefs();
-      jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
-    }
-    else
-    {
-      uniqueSetSuffix = "";
-      jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
-      // overwrite the
-      // view we just
-      // copied
-    }
+    uniqueSetSuffix = "";
+    jm.getJalviewModelSequence().getViewport(0).setId(null);
+    // we don't overwrite the view we just copied
+
     if (this.frefedSequence == null)
     {
-      frefedSequence = new Vector();
+      frefedSequence = new Vector<SeqFref>();
     }
 
     viewportsAdded.clear();
@@ -5382,32 +5354,8 @@ public class Jalview2XML
     return af.alignPanel;
   }
 
-  /**
-   * flag indicating if hashtables should be cleared on finalization TODO this
-   * flag may not be necessary
-   */
-  private final boolean _cleartables = true;
-
   private Hashtable jvids2vobj;
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see java.lang.Object#finalize()
-   */
-  @Override
-  protected void finalize() throws Throwable
-  {
-    // really make sure we have no buried refs left.
-    if (_cleartables)
-    {
-      clearSeqRefs();
-    }
-    this.seqRefIds = null;
-    this.seqsToIds = null;
-    super.finalize();
-  }
-
   private void warn(String msg)
   {
     warn(msg, null);