merge commit

[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 285dcc0..76a1c56 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -20,19 +20,30 @@
  */
 package jalview.ws.jws2;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
 import java.util.List;
 
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.ToolTipManager;
 
-import jalview.datamodel.*;
-import jalview.gui.*;
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Argument;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
 
 /**
  * DOCUMENT ME!
@@ -98,23 +109,23 @@ public class MsaWSClient extends Jws2Client
     if (!(sh.service instanceof MsaWS))
     {
       // redundant at mo - but may change
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      "The Service called \n"
-                              + sh.serviceType
-                              + "\nis not a \nMultiple Sequence Alignment Service !",
-                      "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage("label.service_called_is_not_msa_service",
+                      new String[]
+                      { sh.serviceType }), MessageManager
+              .getString("label.internal_jalview_error"),
+              JOptionPane.WARNING_MESSAGE);
 
       return;
     }
     server = (MsaWS) sh.service;
     if ((wsInfo = setWebService(sh, false)) == null)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-              "The Multiple Sequence Alignment Service named "
-                      + sh.serviceType + " is unknown",
-              "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage("label.msa_service_is_unknown", new String[]
+              { sh.serviceType }), MessageManager
+              .getString("label.internal_jalview_error"),
+              JOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -164,9 +175,57 @@ public class MsaWSClient extends Jws2Client
             WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
             submitGaps, preserveOrder, seqdataset);
     wsInfo.setthisService(msathread);
+    if (isValidAlignment(alignFrame.getCurrentView().getAlignment()))
+    {
+
     msathread.start();
+    }
   }
 
+  private boolean isValidAlignment(AlignmentI seqdataset)
+  {
+    String header = wsInfo.getInfoText()
+            + "\nValidating submited Alignment...";
+    wsInfo.setInfoText(header);
+    int validSeqCount = 0;
+    List<SequenceI> seqs = seqdataset.getSequences();
+    if (seqs.size() < 2)
+    {
+      wsInfo.setInfoText(header
+              + "\nA minimum of two sequences is required to perform this operation");
+      return false;
+    }
+
+    for (SequenceI seq : seqs)
+    {
+
+      if (seq.getSequenceAsString().matches(
+              "([(a-zA-Z?)(-?)(.?)]+)?[a-zA-Z]([(a-zA-Z?)(-?)(.?)]+)?"))
+      {
+        ++validSeqCount;
+      }
+      if (validSeqCount > 1)
+      {
+        wsInfo.setInfoText(header
+                + "\nAlignment sequences was successfully validated");
+        return true;
+      }
+    }
+
+    wsInfo.setInfoText(header
+            + "\nA minimum of two sequences with at least one non-gap character in each sequence is required to perform this operation");
+    return false;
+  }
+
+  public static void main(String[] args)
+  {
+    System.out
+            .println("A"
+                    .matches("([(a-zA-Z?)(-?)(.?)]+)?[a-zA-Z]([(a-zA-Z?)(-?)(.?)]+)?"));
+  }
+
+
+
   protected String getServiceActionKey()
   {
     return "MsaWS";
@@ -276,14 +335,39 @@ public class MsaWSClient extends Jws2Client
                   "label.run_with_preset_params", new String[]
                   { calcName }));
 
+          final int showToolTipFor = ToolTipManager.sharedInstance()
+                  .getDismissDelay();
           for (final WsParamSetI preset : presets)
           {
             final JMenuItem methodR = new JMenuItem(preset.getName());
-            methodR.setToolTipText("<html><p>"
-                    + JvSwingUtils.wrapTooltip("<strong>"
-                            + (preset.isModifiable() ? "User Preset"
-                                    : "Service Preset") + "</strong><br/>"
-                            + preset.getDescription() + "</p>") + "</html>");
+            final int QUICK_TOOLTIP = 1500;
+            // JAL-1582 shorten tooltip display time in these menu items as
+            // they can obscure other options
+            methodR.addMouseListener(new MouseAdapter()
+            {
+              @Override
+              public void mouseEntered(MouseEvent e)
+              {
+                ToolTipManager.sharedInstance().setDismissDelay(
+                        QUICK_TOOLTIP);
+              }
+
+              @Override
+              public void mouseExited(MouseEvent e)
+              {
+                ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
+              }
+
+            });
+            methodR.setToolTipText(JvSwingUtils.wrapTooltip(
+                    true,
+                    "<p><strong>"
+                            + (preset.isModifiable() ? MessageManager
+                                    .getString("label.user_preset")
+                                    : MessageManager
+                                            .getString("label.service_preset"))
+                            + "</strong><br/>" + preset.getDescription()
+                            + "</p>"));
             methodR.addActionListener(new ActionListener()
             {
               public void actionPerformed(ActionEvent e)