X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=37231fd7255ad5d59acccd55309078539402a818;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=2e5ef28bd2cf68b0545ceaeaf7b182b8050eb9be;hpb=26e4138d5fc2cab4f7a52bffbbb1ea802ba44ae4;p=jalview.git
diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 2e5ef28..37231fd 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -1,25 +1,27 @@
/*
- * 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 .
+ * 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.jws2;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.ArrayList;
import java.util.List;
import javax.swing.*;
@@ -28,11 +30,8 @@ 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.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
/**
@@ -48,13 +47,7 @@ public class MsaWSClient extends Jws2Client
*/
MsaWS server;
- AlignFrame alignFrame;
-
- private Preset preset;
-
- private List 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 +57,9 @@ 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,
@@ -90,14 +83,18 @@ public class MsaWSClient extends Jws2Client
* DOCUMENT ME!
*/
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
+ public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
List 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
@@ -111,67 +108,7 @@ public class MsaWSClient extends Jws2Client
return;
}
- server = sh.service;
- if (preset != null)
- {
- if (preset instanceof JabaPreset)
- {
- this.preset = ((JabaPreset) preset).p;
- }
- else if (preset instanceof JabaWsParamSet)
- {
- List newargs = new ArrayList();
- 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,
@@ -271,25 +208,28 @@ public class MsaWSClient extends Jws2Client
rmsawsmenu.add(msawsmenu);
calcName = "";
}
- boolean hasparams = false;
- try
- {
- hasparams = (service.getRunnerConfig().getArguments().size() > 0);
- } catch (Exception e)
- {
-
- }
+ 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()
{
@@ -305,9 +245,12 @@ 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()
{
@@ -324,7 +267,9 @@ public class MsaWSClient extends Jws2Client
List 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)
{