/*
- * 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.
*
*/
package jalview.ws.jws2;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.api.JalviewServiceEndpointProviderI;
+import jalview.ws.api.MultipleSequenceAlignmentI;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.gui.MsaWSThread;
+import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.awt.event.ActionEvent;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.ToolTipManager;
-import compbio.data.msa.MsaWS;
-import compbio.metadata.Argument;
-
/**
- * DOCUMENT ME!
+ * MsaWSClient
+ *
+ * Instantiates web service menu items for multiple alignment services, and
+ * holds logic for constructing a web service thread.
+ *
+ * TODO remove dependency on Jws2Client methods for creating AACon service UI
+ * elements.
*
- * @author $author$
+ * @author Jim Procter et al
* @version $Revision$
*/
-public class MsaWSClient extends Jws2Client
+public class MsaWSClient extends Jws2Client implements WSMenuEntryProviderI
{
/**
- * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+ * server is a proxy class implementing the core methods for submitting,
+ * monitoring and retrieving results from a multiple sequence alignment
+ * service
*/
- MsaWS server;
+ MultipleSequenceAlignmentI server;
- public MsaWSClient(Jws2Instance sh, String altitle,
+ public MsaWSClient(ServiceWithParameters sh, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
- boolean preserveOrder, Alignment seqdataset,
+ boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
{
this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
// TODO Auto-generated constructor stub
}
- public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
+ public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
+ String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
- boolean preserveOrder, Alignment seqdataset,
+ boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
{
this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
* DOCUMENT ME!
*/
- public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
- List<Argument> arguments, boolean editParams, String altitle,
+ public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
+ List<ArgumentI> arguments, boolean editParams, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
- boolean preserveOrder, Alignment seqdataset,
+ boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
{
super(_alignFrame, preset, arguments);
return;
}
- if (!(sh.service instanceof MsaWS))
+ if (!(sh instanceof JalviewServiceEndpointProviderI
+ && ((JalviewServiceEndpointProviderI) sh)
+ .getEndpoint() instanceof MultipleSequenceAlignmentI))
{
// redundant at mo - but may change
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.service_called_is_not_msa_service",
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.service_called_is_not_msa_service",
new String[]
- { sh.serviceType }), MessageManager
- .getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
+ { sh.getName() }),
+ MessageManager.getString("label.internal_jalview_error"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
- server = (MsaWS) sh.service;
+ serviceHandle = sh;
+ server = (MultipleSequenceAlignmentI) ((JalviewServiceEndpointProviderI) sh)
+ .getEndpoint();
if ((wsInfo = setWebService(sh, false)) == null)
{
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.msa_service_is_unknown", new String[]
- { sh.serviceType }), MessageManager
- .getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
+ { sh.getName() }),
+ MessageManager.getString("label.internal_jalview_error"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
-
}
public MsaWSClient()
}
private void startMsaWSClient(String altitle, AlignmentView msa,
- boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+ boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
{
// if (!locateWebService())
// {
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 "
+ "alignment of " + altitle;
}
- MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
- WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
- submitGaps, preserveOrder, seqdataset);
+ MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL,
+ wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps,
+ preserveOrder, seqdataset);
if (msathread.hasValidInput())
{
wsInfo.setthisService(msathread);
}
else
{
- JOptionPane.showMessageDialog(alignFrame,
+ wsInfo.setVisible(false);
+ JvOptionPane.showMessageDialog(alignFrame,
MessageManager.getString("info.invalid_msa_input_mininfo"),
MessageManager.getString("info.invalid_msa_notenough"),
- JOptionPane.INFORMATION_MESSAGE);
- wsInfo.setVisible(false);
+ JvOptionPane.INFORMATION_MESSAGE);
}
}
- public static void main(String[] args)
- {
- System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*"));
- }
-
-
-
protected String getServiceActionKey()
{
return "MsaWS";
return (WebServiceName.indexOf("lustal") > -1); // cheat!
}
+ @Override
public void attachWSMenuEntry(JMenu rmsawsmenu,
- final Jws2Instance service, final AlignFrame alignFrame)
+ final ServiceWithParameters service, final AlignFrame alignFrame)
{
- if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+ if (Jws2ClientFactory.registerAAConWSInstance(rmsawsmenu,
+ service, alignFrame))
{
// Alignment dependent analysis calculation WS gui
return;
}
+ serviceHandle = service;
setWebService(service, true); // headless
+ attachWSMenuEntry(rmsawsmenu, alignFrame);
+ }
+
+ @Override
+ public void attachWSMenuEntry(JMenu wsmenu, AlignFrame alignFrame)
+ {
boolean finished = true, submitGaps = false;
- JMenu msawsmenu = rmsawsmenu;
+ /**
+ * temp variables holding msa service submenu or root service menu
+ */
+ JMenu msawsmenu = wsmenu;
+ JMenu rmsawsmenu = wsmenu;
String svcname = WebServiceName;
if (svcname.endsWith("WS"))
{
rmsawsmenu.add(msawsmenu);
calcName = "";
}
- boolean hasparams = service.hasParameters();
+ boolean hasparams = serviceHandle.hasParameters();
+ ServiceWithParameters service = (ServiceWithParameters) serviceHandle;
do
{
String action = "Align ";
if (submitGaps == true)
{
action = "Realign ";
- msawsmenu = new JMenu(MessageManager.formatMessage(
- "label.realign_with_params", new String[]
+ msawsmenu = new JMenu(MessageManager
+ .formatMessage("label.realign_with_params", new String[]
{ svcname }));
msawsmenu.setToolTipText(MessageManager
.getString("label.align_sequences_to_existing_alignment"));
method.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
if (msa != null)
{
- new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
- true, alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
+ new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
+ true,
+ alignFrame.getViewport().getAlignment().getDataset(),
+ alignFrame);
}
}
// arguments
method = new JMenuItem(
MessageManager.getString("label.edit_settings_and_run"));
- method.setToolTipText(MessageManager
- .getString("label.view_and_change_parameters_before_alignment"));
+ method.setToolTipText(MessageManager.getString(
+ "label.view_and_change_parameters_before_alignment"));
method.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
if (msa != null)
{
- new MsaWSClient(service, null, null, true, alignFrame
- .getTitle(), msa, withGaps, true, alignFrame
- .getViewport().getAlignment().getDataset(), alignFrame);
+ new MsaWSClient(service, null, null, true,
+ alignFrame.getTitle(), msa, withGaps, true,
+ alignFrame.getViewport().getAlignment().getDataset(),
+ alignFrame);
}
}
@Override
public void mouseEntered(MouseEvent e)
{
- ToolTipManager.sharedInstance().setDismissDelay(
- QUICK_TOOLTIP);
+ ToolTipManager.sharedInstance()
+ .setDismissDelay(QUICK_TOOLTIP);
}
@Override
public void mouseExited(MouseEvent e)
{
- ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
+ ToolTipManager.sharedInstance()
+ .setDismissDelay(showToolTipFor);
}
});
- methodR.setToolTipText(JvSwingUtils.wrapTooltip(
- true,
- "<p><strong>"
- + (preset.isModifiable() ? MessageManager
- .getString("label.user_preset")
- : MessageManager
- .getString("label.service_preset"))
- + "</strong><br/>" + preset.getDescription()
- + "</p>"));
+ String tooltip = JvSwingUtils.wrapTooltip(true, "<strong>"
+ + (preset.isModifiable()
+ ? MessageManager.getString("label.user_preset")
+ : MessageManager
+ .getString("label.service_preset"))
+ + "</strong><br/>" + preset.getDescription());
+ methodR.setToolTipText(tooltip);
methodR.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame
if (msa != null)
{
MsaWSClient msac = new MsaWSClient(service, preset,
- alignFrame.getTitle(),
- msa, false, true, alignFrame.getViewport()
- .getAlignment().getDataset(), alignFrame);
+ alignFrame.getTitle(), msa, false, true,
+ alignFrame.getViewport().getAlignment()
+ .getDataset(),
+ alignFrame);
}
}
git://source.jalview.org / jalview.git / blobdiff