JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 39be454..b961cfd 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,7 +22,6 @@ package jalview.ws.jws2;
 
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
@@ -110,8 +109,7 @@ public class MsaWSClient extends Jws2Client
       // redundant at mo - but may change
       JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.service_called_is_not_msa_service",
-                      new String[]
-                      { sh.serviceType }), MessageManager
+                      new String[] { sh.serviceType }), MessageManager
               .getString("label.internal_jalview_error"),
               JOptionPane.WARNING_MESSAGE);
 
@@ -121,8 +119,8 @@ public class MsaWSClient extends Jws2Client
     if ((wsInfo = setWebService(sh, false)) == null)
     {
       JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
-              .formatMessage("label.msa_service_is_unknown", new String[]
-              { sh.serviceType }), MessageManager
+              .formatMessage("label.msa_service_is_unknown",
+                      new String[] { sh.serviceType }), MessageManager
               .getString("label.internal_jalview_error"),
               JOptionPane.WARNING_MESSAGE);
 
@@ -131,7 +129,6 @@ public class MsaWSClient extends Jws2Client
 
     startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
 
-
   }
 
   public MsaWSClient()
@@ -175,47 +172,20 @@ public class MsaWSClient extends Jws2Client
     MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
             WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
             submitGaps, preserveOrder, seqdataset);
-    wsInfo.setthisService(msathread);
-
-    msathread.start();
-
-  }
-
-  private boolean isValidAlignment(AlignmentView av)
-  {
-    int validSeqCount = 0;
-    List<SequenceI> seqs = av.getVisibleAlignment('c').getSequences(); // .getSequences();
-    if (seqs.size() < 2)
+    if (msathread.hasValidInput())
     {
-      JOptionPane
-              .showMessageDialog(
-                      alignFrame,
-                      "A minimum of two sequences is required to perform this operation",
-                      "Invalid selection", JOptionPane.INFORMATION_MESSAGE);
-
-      return false;
+      wsInfo.setthisService(msathread);
+      wsInfo.setVisible(true);
+      msathread.start();
     }
-
-    for (SequenceI seq : seqs)
+    else
     {
-
-      if (seq.getSequenceAsString().matches("(-*[a-zA-Z]-*){3}[a-zA-Z-]*"))
-      {
-        ++validSeqCount;
-      }
-      if (validSeqCount > 1)
-      {
-        return true;
-      }
+      JOptionPane.showMessageDialog(alignFrame,
+              MessageManager.getString("info.invalid_msa_input_mininfo"),
+              MessageManager.getString("info.invalid_msa_notenough"),
+              JOptionPane.INFORMATION_MESSAGE);
+      wsInfo.setVisible(false);
     }
-
-    JOptionPane
-            .showMessageDialog(
-                    alignFrame,
-                    "All selected sequence for this job must have a  minimum of \nthree non-gap character to perform this operation",
-                    "Invalid selection", JOptionPane.INFORMATION_MESSAGE);
-
-    return false;
   }
 
   public static void main(String[] args)
@@ -223,8 +193,6 @@ public class MsaWSClient extends Jws2Client
     System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*"));
   }
 
-
-
   protected String getServiceActionKey()
   {
     return "MsaWS";
@@ -279,8 +247,7 @@ public class MsaWSClient extends Jws2Client
       {
         action = "Realign ";
         msawsmenu = new JMenu(MessageManager.formatMessage(
-                "label.realign_with_params", new String[]
-                { svcname }));
+                "label.realign_with_params", new String[] { svcname }));
         msawsmenu.setToolTipText(MessageManager
                 .getString("label.align_sequences_to_existing_alignment"));
         rmsawsmenu.add(msawsmenu);
@@ -288,11 +255,11 @@ public class MsaWSClient extends Jws2Client
       final boolean withGaps = submitGaps;
 
       JMenuItem method = new JMenuItem(MessageManager.formatMessage(
-              "label.calcname_with_default_settings", new String[]
-              { calcName }));
-      method.setToolTipText(MessageManager.formatMessage(
-              "label.action_with_default_settings", new String[]
-              { action }));
+              "label.calcname_with_default_settings",
+              new String[] { calcName }));
+      method.setToolTipText(MessageManager
+              .formatMessage("label.action_with_default_settings",
+                      new String[] { action }));
 
       method.addActionListener(new ActionListener()
       {
@@ -300,11 +267,11 @@ public class MsaWSClient extends Jws2Client
         {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
 
-          if (msa != null && isValidAlignment(msa))
+          if (msa != null)
           {
-          new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
-                  true, alignFrame.getViewport().getAlignment()
-                          .getDataset(), alignFrame);
+            new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
+                    true, alignFrame.getViewport().getAlignment()
+                            .getDataset(), alignFrame);
           }
 
         }
@@ -324,12 +291,12 @@ public class MsaWSClient extends Jws2Client
           public void actionPerformed(ActionEvent e)
           {
             AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-
-            if (msa != null && isValidAlignment(msa))
+            if (msa != null)
             {
-            new MsaWSClient(service, null, null, true, alignFrame
-                    .getTitle(), msa, withGaps, true, alignFrame
-                    .getViewport().getAlignment().getDataset(), alignFrame);
+              new MsaWSClient(service, null, null, true, alignFrame
+                      .getTitle(), msa, withGaps, true, alignFrame
+                      .getViewport().getAlignment().getDataset(),
+                      alignFrame);
             }
 
           }
@@ -338,9 +305,10 @@ public class MsaWSClient extends Jws2Client
         List<WsParamSetI> presets = service.getParamStore().getPresets();
         if (presets != null && presets.size() > 0)
         {
-          JMenu presetlist = new JMenu(MessageManager.formatMessage(
-                  "label.run_with_preset_params", new String[]
-                  { calcName }));
+          JMenu presetlist = new JMenu(
+                  MessageManager.formatMessage(
+                          "label.run_with_preset_params",
+                          new String[] { calcName }));
 
           final int showToolTipFor = ToolTipManager.sharedInstance()
                   .getDismissDelay();
@@ -362,7 +330,8 @@ public class MsaWSClient extends Jws2Client
               @Override
               public void mouseExited(MouseEvent e)
               {
-                ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
+                ToolTipManager.sharedInstance().setDismissDelay(
+                        showToolTipFor);
               }
 
             });
@@ -382,11 +351,12 @@ public class MsaWSClient extends Jws2Client
                 AlignmentView msa = alignFrame
                         .gatherSequencesForAlignment();
 
-                if (msa != null && isValidAlignment(msa))
+                if (msa != null)
                 {
-                new MsaWSClient(service, preset, alignFrame.getTitle(),
-                        msa, false, true, alignFrame.getViewport()
-                                .getAlignment().getDataset(), alignFrame);
+                  MsaWSClient msac = new MsaWSClient(service, preset,
+                          alignFrame.getTitle(), msa, false, true,
+                          alignFrame.getViewport().getAlignment()
+                                  .getDataset(), alignFrame);
                 }
 
               }