JAL-3878 Fetch sequences for alignment on menu action, not creation.

[jalview.git] / src / jalview / ws2 / operations / AlignmentOperation.java

diff --git a/src/jalview/ws2/operations/AlignmentOperation.java b/src/jalview/ws2/operations/AlignmentOperation.java
index 6a1baf2..14564d6 100644 (file)
--- a/src/jalview/ws2/operations/AlignmentOperation.java
+++ b/src/jalview/ws2/operations/AlignmentOperation.java
@@ -33,6 +33,7 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.Sequence;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.WebserviceInfo;
 import jalview.gui.WsJobParameters;
@@ -69,12 +70,24 @@ public class AlignmentOperation implements Operation
   }
 
   @Override
+  public String getName()
+  {
+    return service.getName();
+  }
+
+  @Override
   public String getTypeName()
   {
     return "Multiple Sequence Alignment";
   }
 
   @Override
+  public String getHostName()
+  {
+    return service.getHostName();
+  }
+
+  @Override
   public int getMinSequences()
   {
     return 2;
@@ -106,6 +119,12 @@ public class AlignmentOperation implements Operation
   }
 
   @Override
+  public boolean isInteractive()
+  {
+    return false;
+  }
+
+  @Override
   public MenuEntryProviderI getMenuBuilder()
   {
     return this::buildMenu;
@@ -137,9 +156,6 @@ public class AlignmentOperation implements Operation
     final String action = submitGaps ? "Align" : "Realign";
     final var calcName = service.getName();
 
-    final AlignmentView msa = frame.gatherSequencesForAlignment();
-    final AlignViewport viewport = frame.getViewport();
-    final AlignmentI alignment = frame.getViewport().getAlignment();
     String title = frame.getTitle();
     WebServiceExecutor executor = frame.getViewport().getWSExecutor();
     {
@@ -148,11 +164,14 @@ public class AlignmentOperation implements Operation
       item.setToolTipText(MessageManager
               .formatMessage("label.action_with_default_settings", action));
       item.addActionListener((event) -> {
+        final AlignmentView msa = frame.gatherSequencesForAlignment();
+        final AlignViewport viewport = frame.getViewport();
+        final AlignmentI alignment = frame.getViewport().getAlignment();
         if (msa != null)
         {
           WebServiceWorkerI worker = new AlignmentWorker(msa,
-                  Collections.emptyList(), title, submitGaps, true,
-                  alignment, viewport);
+              Collections.emptyList(), title, submitGaps, true,
+              alignment, viewport);
           executor.submit(worker);
         }
       });
@@ -166,18 +185,21 @@ public class AlignmentOperation implements Operation
       item.setToolTipText(MessageManager.getString(
               "label.view_and_change_parameters_before_alignment"));
       item.addActionListener((event) -> {
+        final AlignmentView msa = frame.gatherSequencesForAlignment();
+        final AlignViewport viewport = frame.getViewport();
+        final AlignmentI alignment = frame.getViewport().getAlignment();
         if (msa != null)
         {
           openEditParamsDialog(service, null, null)
-                  .thenAcceptAsync((arguments) -> {
-                    if (arguments != null)
-                    {
-                      WebServiceWorkerI worker = new AlignmentWorker(msa,
-                              arguments, title, submitGaps, true, alignment,
-                              viewport);
-                      executor.submit(worker);
-                    }
-                  });
+              .thenAcceptAsync((arguments) -> {
+                if (arguments != null)
+                {
+                  WebServiceWorkerI worker = new AlignmentWorker(msa,
+                      arguments, title, submitGaps, true, alignment,
+                      viewport);
+                  executor.submit(worker);
+                }
+              });
         }
       });
       parent.add(item);
@@ -216,11 +238,14 @@ public class AlignmentOperation implements Operation
                         preset.getDescription()));
         item.setToolTipText(tooltip);
         item.addActionListener((event) -> {
+          final AlignmentView msa = frame.gatherSequencesForAlignment();
+          final AlignViewport viewport = frame.getViewport();
+          final AlignmentI alignment = frame.getViewport().getAlignment();
           if (msa != null)
           {
             WebServiceWorkerI worker = new AlignmentWorker(msa,
-                    preset.getArguments(), title, submitGaps, true,
-                    alignment, viewport);
+                preset.getArguments(), title, submitGaps, true,
+                alignment, viewport);
             executor.submit(worker);
           }
         });
@@ -518,8 +543,9 @@ public class AlignmentOperation implements Operation
       updateWSInfoGlobalStatus();
       if (results.size() > 0)
       {
-        wsInfo.showResultsNewFrame
-                .addActionListener(evt -> displayResults(results));
+        OutputWrapper out = prepareOutput(results);
+        wsInfo.showResultsNewFrame.addActionListener(evt -> displayNewFrame(
+                new Alignment(out.aln), out.alorders, out.hidden));
         wsInfo.setResultsReady();
       }
       else
@@ -529,7 +555,24 @@ public class AlignmentOperation implements Operation
       wsInfo.removeProgressBar(progbarId);
     }
 
-    private void displayResults(Map<Long, AlignmentI> alignments)
+    private class OutputWrapper
+    {
+      AlignmentI aln;
+
+      List<AlignmentOrder> alorders;
+
+      HiddenColumns hidden;
+
+      OutputWrapper(AlignmentI aln, List<AlignmentOrder> alorders,
+              HiddenColumns hidden)
+      {
+        this.aln = aln;
+        this.alorders = alorders;
+        this.hidden = hidden;
+      }
+    }
+
+    private OutputWrapper prepareOutput(Map<Long, AlignmentI> alignments)
     {
       List<AlignmentOrder> alorders = new ArrayList<>();
       SequenceI[][] results = new SequenceI[jobs.size()][];
@@ -538,8 +581,8 @@ public class AlignmentOperation implements Operation
       {
         WSJob job = jobs.get(i);
         AlignmentI aln = alignments.get(job.getUid());
-        if (aln != null)
-        { // equivalent of job.hasResults()
+        if (aln != null) // equivalent of job.hasResults()
+        {
           /* Get the alignment including any empty sequences in the original
            * order with original ids. */
           JobInput input = inputs.get(job.getUid());
@@ -571,6 +614,7 @@ public class AlignmentOperation implements Operation
           // temporary workaround for deuniquify
           @SuppressWarnings({ "rawtypes", "unchecked" })
           Hashtable names = new Hashtable(input.sequenceNames);
+          // FIXME first call to deuniquify alters original alignment
           SeqsetUtils.deuniquify(names, result);
           alorders.add(msaOrder);
           results[i] = result;
@@ -597,8 +641,8 @@ public class AlignmentOperation implements Operation
         aln.setDataset(dataset);
 
       propagateDatasetMappings(aln);
-
-      displayNewFrame(aln, alorders, hidden);
+      return new OutputWrapper(aln, alorders, hidden);
+      // displayNewFrame(aln, alorders, hidden);
     }
 
     /*
@@ -654,6 +698,9 @@ public class AlignmentOperation implements Operation
        * If alignment was requested from one half of a SplitFrame, show in a
        * SplitFrame with the other pane similarly aligned.
        */
+
+      Desktop.addInternalFrame(frame, alnTitle, AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
     }
 
     private List<List<Integer>> sortOrders(List<?> alorders)