From aeb0422c06425ac0c76375106ffc635d03e88b88 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 28 Apr 2005 14:28:43 +0000
Subject: [PATCH] added MuscleWS and did a bit more standardisation of WS
 threads.

---
 src/jalview/gui/AlignFrame.java     |   33 +++++++++++++++++++++++++++++++++
 src/jalview/gui/WebserviceInfo.java |   20 ++++++++++++++++----
 src/jalview/jbgui/GAlignFrame.java  |   13 +++++++++++++
 3 files changed, 62 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b217e9c..1b9ee91 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1188,6 +1188,39 @@ public class AlignFrame extends GAlignFrame
 
     }
   }
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO:resolve which menu item was actually selected
+    // Now, check we have enough sequences
+      if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+      {
+        // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+        SequenceGroup seqs = viewport.getSelectionGroup();
+        int sz;
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+
+        MsaWSClient ct = new jalview.ws.MsaWSClient(msa);
+      }
+      else
+      {
+        Vector seqs = viewport.getAlignment().getSequences();
+
+        if (seqs.size() > 1) {
+          SequenceI[] msa = new SequenceI[seqs.size()];
+          for (int i = 0; i < seqs.size(); i++)
+          {
+            msa[i] = (SequenceI) seqs.elementAt(i);
+          }
+
+          MsaWSClient ct = new MsaWSClient(msa);
+        }
+
+      }
+    }
 
     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
     // Pick the tree file
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 26aa067..7ce77a3 100755
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -17,6 +17,15 @@ public class WebserviceInfo extends GWebserviceInfo
   int angle = 0;
 
   String title="";
+  jalview.ws.WSClientI thisService;
+  boolean serviceIsCancellable;
+  public jalview.ws.WSClientI getthisService() {
+    return thisService;
+  }
+  public void setthisService(jalview.ws.WSClientI newservice) {
+    thisService = newservice;
+    serviceIsCancellable = newservice.isCancellable();
+  }
 
   public WebserviceInfo(String title, String info)
   {
@@ -79,10 +88,13 @@ public class WebserviceInfo extends GWebserviceInfo
 
   protected void cancel_actionPerformed(ActionEvent e)
   {
-    JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                          "Cancel not implemented yet!!" ,
-                                          "Cancel job"
-                                          ,JOptionPane.WARNING_MESSAGE);
+    if (!serviceIsCancellable)
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "Cancel not implemented yet!!" ,
+                                            "Cancel job"
+                                            ,JOptionPane.WARNING_MESSAGE);
+    else
+      thisService.cancelJob();
   }
 
 
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 3630528..3cb11e2 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -42,6 +42,7 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
   protected JMenuItem clustalAlignMenuItem = new JMenuItem();
+  protected JMenuItem msaAlignMenuItem = new JMenuItem();
   BorderLayout borderLayout1 = new BorderLayout();
   public JLabel statusBar = new JLabel();
   protected JMenu saveAlignmentMenu = new JMenu();
@@ -332,6 +333,14 @@ public class GAlignFrame extends JInternalFrame
         clustalAlignMenuItem_actionPerformed(e);
       }
     });
+    msaAlignMenuItem.setText("Muscle alignment");
+    msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        msaAlignMenuItem_actionPerformed(e);
+      }
+    });
     this.getContentPane().setLayout(borderLayout1);
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBackground(Color.white);
@@ -817,6 +826,7 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(avDistanceTreeBlosumMenuItem);
     calculateMenu.add(njTreeBlosumMenuItem);
     alignMenu.add(clustalAlignMenuItem);
+    alignMenu.add(msaAlignMenuItem);
     alignMenu.add(jpred);
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
     jMenu1.add(pasteNew);
@@ -1003,7 +1013,10 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+  {
 
+  }
 
 
   protected void clustalColour_actionPerformed(ActionEvent e)
-- 
1.7.10.2