X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=ebd826e4015d84a2fbace1842b852e876acc9c3a;hb=035fe333749af8d09b517287b4b83c81d5f25fc7;hp=1230abb36118e9fca82a47723c626c16c14129a6;hpb=6b42903480336217a0b8ce9fc1604e686ba3b525;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 1230abb..ebd826e 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -1,39 +1,46 @@
 /*
- * 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.util.ArrayList;
 import java.util.List;
 
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
 
-import jalview.datamodel.*;
-import jalview.gui.*;
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Argument;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
-import jalview.ws.jws2.dm.JabaWsParamSet;
-import jalview.ws.params.WsParamSetI;
 
 /**
  * DOCUMENT ME!
@@ -48,13 +55,7 @@ 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)
@@ -64,9 +65,9 @@ public class MsaWSClient extends Jws2Client
     // TODO Auto-generated constructor stub
   }
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI 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,
@@ -90,94 +91,35 @@ public class MsaWSClient extends Jws2Client
    *          DOCUMENT ME!
    */
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI 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);
+                      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;
-    if (preset != null)
-    {
-      if (preset instanceof JabaPreset)
-      {
-        this.preset = ((JabaPreset) preset).p;
-      }
-      else if (preset instanceof JabaWsParamSet)
-      {
-        List<Argument> newargs = new ArrayList<Argument>();
-        JabaWsParamSet pset = ((JabaWsParamSet) preset);
-        for (Option opt : pset.getjabaArguments())
-        {
-          newargs.add(opt);
-        }
-        if (arguments != null && arguments.size() > 0)
-        {
-          // merge arguments with preset's own arguments.
-          for (Argument opt : arguments)
-          {
-            newargs.add(opt);
-          }
-        }
-        paramset = newargs;
-      }
-      else
-      {
-        throw new Error(
-                "Implementation error: Can only instantiate Jaba parameter sets.");
-      }
-    }
-    else
-    {
-      // just provided with a bunch of arguments
-      this.paramset = arguments;
-    }
-    if (editParams)
-    {
-      if (sh.paramStore == null)
-      {
-        sh.paramStore = new JabaParamStore(sh,
-                Desktop.getUserParameterStore());
-      }
-      WsJobParameters jobParams = new WsJobParameters(sh, preset);
-      if (!jobParams.showRunDialog())
-      {
-        return;
-      }
-      WsParamSetI prset = jobParams.getPreset();
-      if (prset == null)
-      {
-        paramset = JabaParamStore.getJabafromJwsArgs(jobParams
-                .getJobParams());
-      }
-      else
-      {
-        this.preset = ((JabaPreset) prset).p;
-        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);
+    		  MessageManager.formatMessage("label.msa_service_is_unknown", new String[]{sh.serviceType}),
+    		  MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -227,9 +169,57 @@ 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";
@@ -256,6 +246,11 @@ 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;
@@ -274,18 +269,25 @@ public class MsaWSClient extends Jws2Client
     boolean hasparams = service.hasParameters();
     do
     {
-      String action="Align ";
+      String action = "Align ";
       if (submitGaps == true)
       {
-        action="Realign ";
-        msawsmenu = new JMenu("Realign with " + svcname);
-        msawsmenu.setToolTipText("Align sequences to an existing alignment");
+        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(action+"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()
       {
@@ -301,9 +303,12 @@ public class MsaWSClient extends Jws2Client
       msawsmenu.add(method);
       if (hasparams)
       {
-        // only add these menu options if the service has user-modifiable arguments
-        method = new JMenuItem(calcName + "Edit and run ...");
-        method.setToolTipText("View and change the parameters before alignment.");
+        // 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"));
 
         method.addActionListener(new ActionListener()
         {
@@ -320,16 +325,17 @@ public class MsaWSClient extends Jws2Client
         List<WsParamSetI> presets = service.getParamStore().getPresets();
         if (presets != null && presets.size() > 0)
         {
-          JMenu presetlist = new JMenu(calcName + "Presets");
+          JMenu presetlist = new JMenu(MessageManager.formatMessage(
+                  "label.run_with_preset_params", new String[]
+                  { calcName }));
 
           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>");
+            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)