X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=83d6d16aee98d061a4478826b409fc457c9186a5;hb=80238b0ded8d29f9f50399c51bc550bc1df9c426;hp=76a1c56ed89a16f5102e8eb08e476e74ab666b81;hpb=a37f0ae9a4e8c0f318bac29dcf56811e220ee3c6;p=jalview.git diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java index 76a1c56..83d6d16 100644 --- a/src/jalview/ws/jws2/MsaWSClient.java +++ b/src/jalview/ws/jws2/MsaWSClient.java @@ -1,6 +1,6 @@ /* - * 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. * @@ -20,15 +20,19 @@ */ 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.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; @@ -39,28 +43,32 @@ import java.util.List; 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. * - * @author $author$ + * TODO remove dependency on Jws2Client methods for creating AACon service UI + * elements. + * + * @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, @@ -68,9 +76,10 @@ public class MsaWSClient extends Jws2Client // 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, @@ -94,10 +103,10 @@ public class MsaWSClient extends Jws2Client * DOCUMENT ME! */ - public MsaWSClient(Jws2Instance sh, WsParamSetI preset, - List arguments, boolean editParams, String altitle, + public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset, + List 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); @@ -106,29 +115,35 @@ public class MsaWSClient extends Jws2Client 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); } @@ -140,7 +155,7 @@ public class MsaWSClient extends Jws2Client } private void startMsaWSClient(String altitle, AlignmentView msa, - boolean submitGaps, boolean preserveOrder, Alignment seqdataset) + boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset) { // if (!locateWebService()) // { @@ -152,9 +167,8 @@ public class MsaWSClient extends Jws2Client 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 " @@ -171,61 +185,30 @@ public class MsaWSClient extends Jws2Client + "alignment of " + altitle; } - MsaWSThread msathread = new MsaWSThread(server, preset, paramset, - WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa, - submitGaps, preserveOrder, seqdataset); - wsInfo.setthisService(msathread); - if (isValidAlignment(alignFrame.getCurrentView().getAlignment())) + MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL, + wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps, + preserveOrder, seqdataset); + if (msathread.hasValidInput()) { - - msathread.start(); + wsInfo.setthisService(msathread); + wsInfo.setVisible(true); + msathread.start(); } - } - - private boolean isValidAlignment(AlignmentI seqdataset) - { - String header = wsInfo.getInfoText() - + "\nValidating submited Alignment..."; - wsInfo.setInfoText(header); - int validSeqCount = 0; - List seqs = seqdataset.getSequences(); - if (seqs.size() < 2) + else { - wsInfo.setInfoText(header - + "\nA minimum of two sequences is required to perform this operation"); - return false; + JvOptionPane.showMessageDialog(alignFrame, + MessageManager.getString("info.invalid_msa_input_mininfo"), + MessageManager.getString("info.invalid_msa_notenough"), + JvOptionPane.INFORMATION_MESSAGE); + wsInfo.setVisible(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?)(-?)(.?)]+)?")); + System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*")); } - - protected String getServiceActionKey() { return "MsaWS"; @@ -249,17 +232,30 @@ public class MsaWSClient extends Jws2Client 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 (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")) { @@ -272,15 +268,16 @@ public class MsaWSClient extends Jws2Client 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")); @@ -297,12 +294,18 @@ public class MsaWSClient extends Jws2Client method.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { AlignmentView msa = alignFrame.gatherSequencesForAlignment(); - new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps, - true, alignFrame.getViewport().getAlignment() - .getDataset(), alignFrame); + + if (msa != null) + { + new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps, + true, + alignFrame.getViewport().getAlignment().getDataset(), + alignFrame); + } } }); @@ -313,17 +316,22 @@ public class MsaWSClient extends Jws2Client // 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(); - new MsaWSClient(service, null, null, true, alignFrame - .getTitle(), msa, withGaps, true, alignFrame - .getViewport().getAlignment().getDataset(), alignFrame); + if (msa != null) + { + new MsaWSClient(service, null, null, true, + alignFrame.getTitle(), msa, withGaps, true, + alignFrame.getViewport().getAlignment().getDataset(), + alignFrame); + } } }); @@ -348,35 +356,41 @@ public class MsaWSClient extends Jws2Client @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, - "

" - + (preset.isModifiable() ? MessageManager - .getString("label.user_preset") - : MessageManager - .getString("label.service_preset")) - + "
" + preset.getDescription() - + "

")); + String tooltip = JvSwingUtils.wrapTooltip(true, "" + + (preset.isModifiable() + ? MessageManager.getString("label.user_preset") + : MessageManager + .getString("label.service_preset")) + + "
" + preset.getDescription()); + methodR.setToolTipText(tooltip); methodR.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { AlignmentView msa = alignFrame .gatherSequencesForAlignment(); - new MsaWSClient(service, preset, alignFrame.getTitle(), - msa, false, true, alignFrame.getViewport() - .getAlignment().getDataset(), alignFrame); + + if (msa != null) + { + MsaWSClient msac = new MsaWSClient(service, preset, + alignFrame.getTitle(), msa, false, true, + alignFrame.getViewport().getAlignment() + .getDataset(), + alignFrame); + } }