/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
- *
+ *
* 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/>.
+ * 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.*;
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.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
/**
*/
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)
// 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,
* 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
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,
boolean hasparams = service.hasParameters();
do
{
- String action="Align ";
+ String action = "Align ";
if (submitGaps == true)
{
- action="Realign ";
+ action = "Realign ";
msawsmenu = new JMenu("Realign with " + svcname);
- msawsmenu.setToolTipText("Align sequences to an existing alignment");
+ msawsmenu
+ .setToolTipText("Align sequences to an 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(calcName + "with Defaults");
+ method.setToolTipText(action + "with default settings");
method.addActionListener(new ActionListener()
{
msawsmenu.add(method);
if (hasparams)
{
- // only add these menu options if the service has user-modifiable arguments
- method = new JMenuItem(calcName + "Edit and run ...");
+ // only add these menu options if the service has user-modifiable
+ // arguments
+ method = new JMenuItem("Edit settings and run ...");
method.setToolTipText("View and change the parameters before alignment.");
method.addActionListener(new ActionListener()
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu(calcName + "Presets");
+ JMenu presetlist = new JMenu("Run " + calcName + "with preset");
for (final WsParamSetI preset : presets)
{
git://source.jalview.org / jalview.git / blobdiff