JAL-2446 merged to spike branch

[jalview.git] / src / jalview / ws / jws2 / MsaWSThread.java

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index e2f3a7c..2187f46 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -26,7 +26,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -176,6 +176,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
      * 
      * @return true if getAlignment will return a valid alignment result.
      */
+    @Override
     public boolean hasResults()
     {
       if (subjobComplete
@@ -316,6 +317,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
      * 
      * @return boolean true if job can be submitted.
      */
+    @Override
     public boolean hasValidInput()
     {
       // TODO: get attributes for this MsaWS instance to check if it can do two
@@ -436,7 +438,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
   String alTitle; // name which will be used to form new alignment window.
 
-  Alignment dataset; // dataset to which the new alignment will be
+  AlignmentI dataset; // dataset to which the new alignment will be
 
   // associated.
 
@@ -479,7 +481,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
           String wsUrl, WebserviceInfo wsinfo,
           jalview.gui.AlignFrame alFrame, String wsname, String title,
           AlignmentView _msa, boolean subgaps, boolean presorder,
-          Alignment seqset)
+          AlignmentI seqset)
   {
     this(server2, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
     OutputHeader = wsInfo.getProgressText();
@@ -530,11 +532,13 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     return validInput;
   }
 
+  @Override
   public boolean isCancellable()
   {
     return true;
   }
 
+  @Override
   public void cancelJob()
   {
     if (!jobComplete && jobs != null)
@@ -605,6 +609,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     }
   }
 
+  @Override
   public void pollJob(AWsJob job) throws Exception
   {
     // TODO: investigate if we still need to cast here in J1.6
@@ -650,6 +655,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     return changed;
   }
 
+  @Override
   public void StartJob(AWsJob job)
   {
     Exception lex = null;
@@ -775,6 +781,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     }
   }
 
+  @Override
   public void parseResult()
   {
     long progbar = System.currentTimeMillis();
@@ -889,6 +896,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       wsInfo.showResultsNewFrame
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(true);
@@ -897,6 +905,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       wsInfo.mergeResults
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(false);
@@ -952,7 +961,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       orders[j] = null;
     }
     SequenceI[] alignment = (SequenceI[]) newview[0];
-    ColumnSelection columnselection = (ColumnSelection) newview[1];
+    HiddenColumns hidden = (HiddenColumns) newview[1];
     Alignment al = new Alignment(alignment);
     // TODO: add 'provenance' property to alignment from the method notes
     if (lastProgram != null)
@@ -970,7 +979,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
     if (newFrame)
     {
-      displayInNewFrame(al, alorders, columnselection);
+      displayInNewFrame(al, alorders, hidden);
 
     }
     else
@@ -991,9 +1000,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI
    * @param columnselection
    */
   protected void displayInNewFrame(AlignmentI al,
-          List<AlignmentOrder> alorders, ColumnSelection columnselection)
+          List<AlignmentOrder> alorders, HiddenColumns hidden)
   {
-    AlignFrame af = new AlignFrame(al, columnselection,
+    AlignFrame af = new AlignFrame(al, hidden,
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
     // initialise with same renderer settings as in parent alignframe.
@@ -1023,6 +1032,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       // becomes null if the alignment window was closed before the alignment
       // job finished.
       AlignmentI copyComplement = new Alignment(complement);
+      // todo should this be done by copy constructor?
+      copyComplement.setGapCharacter(complement.getGapCharacter());
+      // share the same dataset (and the mappings it holds)
+      copyComplement.setDataset(complement.getDataset());
       copyComplement.alignAs(al);
       if (copyComplement.getHeight() > 0)
       {
@@ -1101,6 +1114,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     }
   }
 
+  @Override
   public boolean canMergeResults()
   {
     return false;