X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fjws1%2FMsaWSClient.java;h=4a096259d3bc2c0fa057e8dfff4532cc7e0d1e41;hb=2b6a74893883a246d40a99a2e981ef6cad4fed5a;hp=91374f1d9cb4b4cbf38aaab9e71bd1da46a734f0;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/ws/jws1/MsaWSClient.java b/src/jalview/ws/jws1/MsaWSClient.java
index 91374f1..4a09625 100644
--- a/src/jalview/ws/jws1/MsaWSClient.java
+++ b/src/jalview/ws/jws1/MsaWSClient.java
@@ -1,31 +1,42 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
-import ext.vamsas.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import ext.vamsas.MuscleWSServiceLocator;
+import ext.vamsas.MuscleWSSoapBindingStub;
+import ext.vamsas.ServiceHandle;
/**
* DOCUMENT ME!
@@ -60,31 +71,31 @@ public class MsaWSClient extends WS1Client
public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
- boolean preserveOrder, Alignment seqdataset,
+ boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
{
super();
alignFrame = _alignFrame;
if (!sh.getAbstractName().equals("MsaWS"))
{
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- "The Service called \n"
- + sh.getName()
- + "\nis not a \nMultiple Sequence Alignment Service !",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.service_called_is_not_msa_service",
+ new String[]
+ { sh.getName() }),
+ MessageManager.getString("label.internal_jalview_error"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
if ((wsInfo = setWebService(sh)) == null)
{
- JOptionPane.showMessageDialog(
- Desktop.desktop,
- "The Multiple Sequence Alignment Service named "
- + sh.getName() + " is unknown",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.msa_service_is_unknown", new String[]
+ { sh.getName() }),
+ MessageManager.getString("label.internal_jalview_error"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
@@ -99,7 +110,7 @@ public class MsaWSClient extends WS1Client
}
private void startMsaWSClient(String altitle, AlignmentView msa,
- boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+ boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
{
if (!locateWebService())
{
@@ -111,9 +122,8 @@ public class MsaWSClient extends WS1Client
String jobtitle = WebServiceName.toLowerCase();
if (jobtitle.endsWith("alignment"))
{
- if (submitGaps
- && (!jobtitle.endsWith("realignment") || jobtitle
- .indexOf("profile") == -1))
+ if (submitGaps && (!jobtitle.endsWith("realignment")
+ || jobtitle.indexOf("profile") == -1))
{
int pos = jobtitle.indexOf("alignment");
jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
@@ -149,7 +159,7 @@ public class MsaWSClient extends WS1Client
try
{
- this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+ this.server = loc.getMuscleWS(new java.net.URL(WsURL));
((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute
// timeout
} catch (Exception ex)
@@ -191,6 +201,7 @@ public class MsaWSClient extends WS1Client
return (WebServiceName.indexOf("lustal") > -1); // cheat!
}
+ @Override
public void attachWSMenuEntry(JMenu msawsmenu,
final ServiceHandle serviceHandle, final AlignFrame alignFrame)
{
@@ -199,12 +210,14 @@ public class MsaWSClient extends WS1Client
method.setToolTipText(WsURL);
method.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new jalview.ws.jws1.MsaWSClient(serviceHandle, alignFrame
- .getTitle(), msa, false, true, alignFrame.getViewport()
- .getAlignment().getDataset(), alignFrame);
+ new jalview.ws.jws1.MsaWSClient(serviceHandle,
+ alignFrame.getTitle(), msa, false, true,
+ alignFrame.getViewport().getAlignment().getDataset(),
+ alignFrame);
}
@@ -213,17 +226,19 @@ public class MsaWSClient extends WS1Client
if (canSubmitGaps())
{
// We know that ClustalWS can accept partial alignments for refinement.
- final JMenuItem methodR = new JMenuItem(serviceHandle.getName()
- + " Realign");
+ final JMenuItem methodR = new JMenuItem(
+ serviceHandle.getName() + " Realign");
methodR.setToolTipText(WsURL);
methodR.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new jalview.ws.jws1.MsaWSClient(serviceHandle, alignFrame
- .getTitle(), msa, true, true, alignFrame.getViewport()
- .getAlignment().getDataset(), alignFrame);
+ new jalview.ws.jws1.MsaWSClient(serviceHandle,
+ alignFrame.getTitle(), msa, true, true,
+ alignFrame.getViewport().getAlignment().getDataset(),
+ alignFrame);
}