X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FSeqSearchWSClient.java;h=eb60813cc3ef80414272406a072d7d1e98a22022;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=8cd2fe125aa9cf97e5138a9ceeaf3291f9850c66;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/ws/jws1/SeqSearchWSClient.java b/src/jalview/ws/jws1/SeqSearchWSClient.java
index 8cd2fe1..eb60813 100644
--- a/src/jalview/ws/jws1/SeqSearchWSClient.java
+++ b/src/jalview/ws/jws1/SeqSearchWSClient.java
@@ -1,22 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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.bin.Cache;
+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.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
@@ -25,11 +37,12 @@ import java.util.Hashtable;
import java.util.StringTokenizer;
import java.util.Vector;
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
-import ext.vamsas.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import ext.vamsas.SeqSearchServiceLocator;
+import ext.vamsas.SeqSearchServiceSoapBindingStub;
+import ext.vamsas.ServiceHandle;
/**
* DOCUMENT ME!
@@ -64,7 +77,7 @@ public class SeqSearchWSClient extends WS1Client
public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,
jalview.datamodel.AlignmentView msa, String db,
- Alignment seqdataset, AlignFrame _alignFrame)
+ AlignmentI seqdataset, AlignFrame _alignFrame)
{
super();
alignFrame = _alignFrame;
@@ -72,20 +85,25 @@ public class SeqSearchWSClient extends WS1Client
// name to service client name
if (!sh.getAbstractName().equals(this.getServiceActionKey()))
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- "The Service called \n" + sh.getName()
- + "\nis not a \nSequence Search Service !",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.service_called_is_not_seq_search_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 Sequence Search Service named " + sh.getName()
- + " is unknown", "Internal Jalview Error",
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.seq_search_service_is_unknown", new String[]
+ { sh.getName() }),
+ MessageManager.getString("label.internal_jalview_error"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
@@ -112,7 +130,7 @@ public class SeqSearchWSClient extends WS1Client
}
private void startSeqSearchClient(String altitle, AlignmentView msa,
- String db, Alignment seqdataset)
+ String db, AlignmentI seqdataset)
{
if (!locateWebService())
{
@@ -123,20 +141,21 @@ public class SeqSearchWSClient extends WS1Client
// sequence db
boolean profileSearch = msa.getSequences().length > 2 ? true : false;
// single sequence or profile from alignment view
- wsInfo.setProgressText("Searching "
- + visdb
- + (!profileSearch ? " with sequence "
- + msa.getSequences()[0].getRefSeq().getName()
- : " with profile") + " from " + altitle
- + "\nJob details\n");
+ wsInfo.setProgressText("Searching " + visdb
+ + (!profileSearch
+ ? " with sequence "
+ + msa.getSequences()[0].getRefSeq().getName()
+ : " with profile")
+ + " from " + altitle + "\nJob details\n");
String jobtitle = WebServiceName
+ ((WebServiceName.indexOf("earch") > -1) ? " " : " search ")
- + " of "
- + visdb
- + (!profileSearch ? " with sequence "
- + msa.getSequences()[0].getRefSeq().getName()
- : " with profile") + " from " + altitle;
+ + " of " + visdb
+ + (!profileSearch
+ ? " with sequence "
+ + msa.getSequences()[0].getRefSeq().getName()
+ : " with profile")
+ + " from " + altitle;
SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL,
wsInfo, alignFrame, WebServiceName, jobtitle, msa, db,
seqdataset);
@@ -157,8 +176,7 @@ public class SeqSearchWSClient extends WS1Client
try
{
- this.server = (SeqSearchI) loc.getSeqSearchService(new java.net.URL(
- WsURL));
+ this.server = loc.getSeqSearchService(new java.net.URL(WsURL));
((SeqSearchServiceSoapBindingStub) this.server).setTimeout(60000); // One
// minute
// timeout
@@ -205,13 +223,14 @@ public class SeqSearchWSClient extends WS1Client
}
if (!locateWebService())
{
- throw new Exception("Cannot contact service endpoint at " + WsURL);
+ throw new Exception(MessageManager.formatMessage(
+ "exception.cannot_contact_service_endpoint_at", new String[]
+ { WsURL }));
}
String database = server.getDatabase();
if (database == null)
{
- dbParamsForEndpoint.put(WsURL, new String[]
- {});
+ dbParamsForEndpoint.put(WsURL, new String[] {});
return null;
}
StringTokenizer en = new StringTokenizer(database.trim(), ",| ");
@@ -224,6 +243,7 @@ public class SeqSearchWSClient extends WS1Client
return dbs;
}
+ @Override
public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
final AlignFrame af)
{
@@ -241,8 +261,8 @@ public class SeqSearchWSClient extends WS1Client
JMenu defmenu = (JMenu) dbsrchs.get("Default Database");
if (defmenu == null)
{
- dbsrchs.put("Default Database", defmenu = new JMenu(
- "Default Database"));
+ dbsrchs.put("Default Database",
+ defmenu = new JMenu("Default Database"));
newdbsrch.addElement(defmenu);
}
@@ -253,9 +273,10 @@ public class SeqSearchWSClient extends WS1Client
.getSupportedDatabases();
} catch (Exception e)
{
- jalview.bin.Cache.log.warn(
+ Cache.warn(
"Database list request failed, so disabling SeqSearch Service client "
- + sh.getName() + " at " + sh.getEndpointURL(), e);
+ + sh.getName() + " at " + sh.getEndpointURL(),
+ e);
return;
}
JMenuItem method;
@@ -264,6 +285,7 @@ public class SeqSearchWSClient extends WS1Client
method.setToolTipText(sh.getEndpointURL());
method.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// use same input gatherer as for secondary structure prediction
@@ -288,6 +310,7 @@ public class SeqSearchWSClient extends WS1Client
final String searchdb = dbs[db];
method.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();