X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=76a1c56ed89a16f5102e8eb08e476e74ab666b81;hb=a37f0ae9a4e8c0f318bac29dcf56811e220ee3c6;hp=820dfb456d0e9b53ac1cd8149655947a3bd940cc;hpb=b26ca522d2067ef5a4078c99458e7aeb4b44a268;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 820dfb4..76a1c56 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -1,35 +1,49 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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 compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
 
 /**
  * DOCUMENT ME!
@@ -44,13 +58,7 @@ public class MsaWSClient extends Jws2Client
    */
   MsaWS server;
 
-  AlignFrame alignFrame;
-
-  private Preset preset;
-
-  private List<Argument> paramset;
-
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, String altitle,
+  public MsaWSClient(Jws2Instance sh, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
           boolean preserveOrder, Alignment seqdataset,
           AlignFrame _alignFrame)
@@ -60,9 +68,9 @@ public class MsaWSClient extends Jws2Client
     // TODO Auto-generated constructor stub
   }
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset,
-          String altitle, jalview.datamodel.AlignmentView msa,
-          boolean submitGaps, boolean preserveOrder, Alignment seqdataset,
+  public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
+          jalview.datamodel.AlignmentView msa, boolean submitGaps,
+          boolean preserveOrder, Alignment seqdataset,
           AlignFrame _alignFrame)
   {
     this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
@@ -86,51 +94,38 @@ public class MsaWSClient extends Jws2Client
    *          DOCUMENT ME!
    */
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset,
+  public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
           List<Argument> arguments, boolean editParams, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
           boolean preserveOrder, Alignment seqdataset,
           AlignFrame _alignFrame)
   {
-    super();
-    alignFrame = _alignFrame;
+    super(_alignFrame, preset, arguments);
+    if (!processParams(sh, editParams))
+    {
+      return;
+    }
+
     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 = sh.service;
-    this.preset = preset;
-    this.paramset = arguments;
-    if (editParams)
-    {
-      WsJobParameters jobParams = new WsJobParameters(sh, preset);
-      if (!jobParams.showRunDialog())
-      {
-        return;
-      }
-      if ((this.preset = jobParams.getPreset())==null)
-      {
-        paramset = jobParams.getJobParams();
-      } else {
-        paramset = null; // no user supplied parameters.
-      }
-    }
-
+    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;
     }
@@ -180,9 +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";
@@ -209,13 +252,18 @@ public class MsaWSClient extends Jws2Client
   public void attachWSMenuEntry(JMenu rmsawsmenu,
           final Jws2Instance service, final AlignFrame alignFrame)
   {
+    if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+    {
+      // Alignment dependent analysis calculation WS gui
+      return;
+    }
     setWebService(service, true); // headless
     boolean finished = true, submitGaps = false;
     JMenu msawsmenu = rmsawsmenu;
     String svcname = WebServiceName;
     if (svcname.endsWith("WS"))
     {
-      svcname = svcname.substring(0,svcname.length()-2);
+      svcname = svcname.substring(0, svcname.length() - 2);
     }
     String calcName = svcname + " ";
     if (canSubmitGaps())
@@ -224,17 +272,28 @@ public class MsaWSClient extends Jws2Client
       rmsawsmenu.add(msawsmenu);
       calcName = "";
     }
-
+    boolean hasparams = service.hasParameters();
     do
     {
+      String action = "Align ";
       if (submitGaps == true)
       {
-        msawsmenu = new JMenu("profile " + svcname);
+        action = "Realign ";
+        msawsmenu = new JMenu(MessageManager.formatMessage(
+                "label.realign_with_params", new String[]
+                { svcname }));
+        msawsmenu.setToolTipText(MessageManager
+                .getString("label.align_sequences_to_existing_alignment"));
         rmsawsmenu.add(msawsmenu);
       }
       final boolean withGaps = submitGaps;
-      JMenuItem method = new JMenuItem(calcName + "Defaults");
-      method.setToolTipText("Align with default settings");
+
+      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 }));
 
       method.addActionListener(new ActionListener()
       {
@@ -248,45 +307,84 @@ public class MsaWSClient extends Jws2Client
         }
       });
       msawsmenu.add(method);
-      method = new JMenuItem(calcName + "Edit and run ...");
-      method.setToolTipText("View and change the parameters before alignment.");
-
-      method.addActionListener(new ActionListener()
+      if (hasparams)
       {
-        public void actionPerformed(ActionEvent e)
-        {
-          AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-          new MsaWSClient(service, null, null, true, alignFrame.getTitle(),
-                  msa, withGaps, true, alignFrame.getViewport()
-                          .getAlignment().getDataset(), alignFrame);
+        // only add these menu options if the service has user-modifiable
+        // arguments
+        method = new JMenuItem(
+                MessageManager.getString("label.edit_settings_and_run"));
+        method.setToolTipText(MessageManager
+                .getString("label.view_and_change_parameters_before_alignment"));
 
-        }
-      });
-      msawsmenu.add(method);
-      PresetManager presets = service.getPresets();
-      if (presets != null && presets.getPresets().size() > 0)
-      {
-        JMenu presetlist = new JMenu(calcName + "Presets");
+        method.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+            new MsaWSClient(service, null, null, true, alignFrame
+                    .getTitle(), msa, withGaps, true, alignFrame
+                    .getViewport().getAlignment().getDataset(), alignFrame);
 
-        for (final Preset preset : (List<Preset>) presets.getPresets())
+          }
+        });
+        msawsmenu.add(method);
+        List<WsParamSetI> presets = service.getParamStore().getPresets();
+        if (presets != null && presets.size() > 0)
         {
-          final JMenuItem methodR = new JMenuItem(preset.getName());
-          methodR.setToolTipText("<html><p>"+preset.getDescription()+"</p></html>");
-          methodR.addActionListener(new ActionListener()
+          JMenu presetlist = new JMenu(MessageManager.formatMessage(
+                  "label.run_with_preset_params", new String[]
+                  { calcName }));
+
+          final int showToolTipFor = ToolTipManager.sharedInstance()
+                  .getDismissDelay();
+          for (final WsParamSetI preset : presets)
           {
-            public void actionPerformed(ActionEvent e)
+            final JMenuItem methodR = new JMenuItem(preset.getName());
+            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()
             {
-              AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-              new MsaWSClient(service, preset, alignFrame.getTitle(), msa,
-                      false, true, alignFrame.getViewport().getAlignment()
-                              .getDataset(), alignFrame);
+              public void actionPerformed(ActionEvent e)
+              {
+                AlignmentView msa = alignFrame
+                        .gatherSequencesForAlignment();
+                new MsaWSClient(service, preset, alignFrame.getTitle(),
+                        msa, false, true, alignFrame.getViewport()
+                                .getAlignment().getDataset(), alignFrame);
 
-            }
+              }
 
-          });
-          presetlist.add(methodR);
+            });
+            presetlist.add(methodR);
+          }
+          msawsmenu.add(presetlist);
         }
-        msawsmenu.add(presetlist);
       }
       if (!submitGaps && canSubmitGaps())
       {