/*
- * 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!
*/
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
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) {
- JabaWsParamSet pset = ((JabaWsParamSet)preset);
- if (arguments!=null && arguments.size()>0)
- {
- // merge arguments with preset's own arguments.
- List<Argument> oldargs = arguments;
- arguments = new ArrayList<Argument>();
- for (Option opt : pset.getjabaArguments()) {
- arguments.add(opt);
- }
- for (Argument opt: oldargs)
- {
- arguments.add(opt);
- }
- }
-
- }else{
- throw new Error("Implementation error: Can only instantiate Jaba parameter sets.");
- }
- }
- this.paramset = arguments;
- if (editParams)
- {
- if (sh.paramStore==null)
- {
- sh.paramStore = new JabaParamStore(sh);
- }
- 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;
}
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";
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;
rmsawsmenu.add(msawsmenu);
calcName = "";
}
-
+ 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()
{
}
});
msawsmenu.add(method);
- method = new JMenuItem(calcName + "Edit and run ...");
- method.setToolTipText("View and change the parameters before alignment.");
-
- method.addActionListener(new ActionListener()
+ if (hasparams)
{
- public void actionPerformed(ActionEvent e)
- {
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, null, null, true, alignFrame.getTitle(),
- msa, withGaps, true, alignFrame.getViewport()
- .getAlignment().getDataset(), alignFrame);
+ // 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"));
- }
- });
- msawsmenu.add(method);
- List<WsParamSetI> presets = service.getParamStore().getPresets();
- if (presets != null && presets.size() > 0)
- {
- JMenu presetlist = new JMenu(calcName + "Presets");
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+ new MsaWSClient(service, null, null, true, alignFrame
+ .getTitle(), msa, withGaps, true, alignFrame
+ .getViewport().getAlignment().getDataset(), alignFrame);
- for (final WsParamSetI preset : presets)
+ }
+ });
+ msawsmenu.add(method);
+ List<WsParamSetI> presets = service.getParamStore().getPresets();
+ if (presets != null && presets.size() > 0)
{
- final JMenuItem methodR = new JMenuItem(preset.getName());
- methodR.setToolTipText("<html><p><strong>"
- + (preset.isModifiable() ? "User Preset"
- : "Service Preset") + "</strong><br/>"
- + preset.getDescription() + "</p></html>");
- methodR.addActionListener(new ActionListener()
+ JMenu presetlist = new JMenu(MessageManager.formatMessage(
+ "label.run_with_preset_params", new String[]
+ { calcName }));
+
+ for (final WsParamSetI preset : presets)
{
- public void actionPerformed(ActionEvent e)
+ final JMenuItem methodR = new JMenuItem(preset.getName());
+ 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()
{
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, preset, alignFrame.getTitle(), msa,
- false, true, alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = alignFrame
+ .gatherSequencesForAlignment();
+ new MsaWSClient(service, preset, alignFrame.getTitle(),
+ msa, false, true, alignFrame.getViewport()
+ .getAlignment().getDataset(), alignFrame);
- }
+ }
- });
- presetlist.add(methodR);
+ });
+ presetlist.add(methodR);
+ }
+ msawsmenu.add(presetlist);
}
- msawsmenu.add(presetlist);
}
if (!submitGaps && canSubmitGaps())
{
git://source.jalview.org / jalview.git / blobdiff