X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2FMsaWSClient.java;h=999fc96406fa3f2a3c648d76d3b7cd9b23d1e2d1;hb=521ce3c96d5977a9bd941894eda7a13dd09deea9;hp=479f22f1e1454d0a41b724e72a30189e0e17afd6;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 479f22f..999fc96 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -43,6 +43,7 @@ public class MsaWSClient
    * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
    */
   ext.vamsas.MuscleWS server;
+  AlignFrame alignFrame;
 
 
   /**
@@ -56,10 +57,14 @@ public class MsaWSClient
    * @param preserveOrder DOCUMENT ME!
    */
 
-  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle, SequenceI[] msa,
-                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
+                     SequenceI[] msa,
+                     boolean submitGaps, boolean preserveOrder,
+                     Alignment seqdataset,
+                     AlignFrame _alignFrame)
   {
 
+    alignFrame = _alignFrame;
     if (!sh.getAbstractName().equals("MsaWS"))
     {
       JOptionPane.showMessageDialog(Desktop.desktop,
@@ -274,6 +279,21 @@ public class MsaWSClient
           if (result.isFinished())
           {
             wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+            wsInfo.showResultsNewFrame.addActionListener(new java.awt.event.ActionListener()
+                {
+                  public void actionPerformed(java.awt.event.ActionEvent evt)
+                  {
+                    displayResults(true);
+                  }
+                });
+           wsInfo.mergeResults.addActionListener(new java.awt.event.ActionListener()
+                {
+                  public void actionPerformed(java.awt.event.ActionEvent evt)
+                  {
+                    displayResults(false);
+                  }
+                });
+           wsInfo.setResultsReady();
             parseResult();
             jobComplete = true;
             jobsRunning--;
@@ -425,7 +445,6 @@ public class MsaWSClient
 
     void parseResult()
     {
-      SequenceI[] seqs = null;
 
       try
       {
@@ -451,41 +470,62 @@ public class MsaWSClient
             OutputHeader += (lines[line] + "\n");
           }
 
-          // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
-          seqs = getVamsasAlignment(result.getMsa());
+          // JBPNote The returned files from a webservice could be
+          // hidden behind icons in the monitor window that,
+          // when clicked, pop up their corresponding data
         }
 
         wsInfo.setProgressText(OutputHeader);
-
-        if (seqs != null)
-        {
-          AlignmentOrder msaorder = new AlignmentOrder(seqs);
-
-          if (preserveOrder)
-          {
-            jalview.analysis.AlignmentSorter.recoverOrder(seqs);
-          }
-
-          jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
-
-          Alignment al = new Alignment(seqs);
-          if (dataset!=null) {
-            al.setDataset(dataset);
-          }
-          // TODO: JBPNote Should also rename the query sequence sometime...
-          AlignFrame af = new AlignFrame(al);
-          af.addSortByOrderMenuItem(ServiceName + " Ordering",
-                                    msaorder);
-
-          Desktop.addInternalFrame(af, alTitle,
-                                   AlignFrame.NEW_WINDOW_WIDTH,
-                                   AlignFrame.NEW_WINDOW_HEIGHT);
-        }
       }
       catch (Exception ex)
       {
         ex.printStackTrace();
       }
     }
+
+    void displayResults(boolean newFrame)
+    {
+      SequenceI [] seqs = getVamsasAlignment(result.getMsa());
+
+      if (seqs != null)
+       {
+         AlignmentOrder msaorder = new AlignmentOrder(seqs);
+
+         if (preserveOrder)
+         {
+           jalview.analysis.AlignmentSorter.recoverOrder(seqs);
+         }
+
+         jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
+
+         Alignment al = new Alignment(seqs);
+         if (dataset!=null)
+         {
+           al.setDataset(dataset);
+         }
+
+         if(newFrame)
+         {
+           // TODO: JBPNote Should also rename the query sequence sometime...
+           AlignFrame af = new AlignFrame(al);
+
+         //>>>This is a fix for the moment, until a better solution is found!!<<<
+           af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
+
+           af.addSortByOrderMenuItem(ServiceName + " Ordering",
+                                     msaorder);
+
+           Desktop.addInternalFrame(af, alTitle,
+                                    AlignFrame.NEW_WINDOW_WIDTH,
+                                    AlignFrame.NEW_WINDOW_HEIGHT);
+
+         }
+         else
+         {
+           System.out.println("MERGE WITH OLD FRAME");
+
+         }
+       }
+    }
   }
 }