X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=8ed4a36ad37ea455bf3ba9de93602fd6ca7ef09d;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=49a34129deaec8dec44acaf0934fb5c84730cb8e;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java index 49a3412..8ed4a36 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 2.8.2b1) - * 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. * @@ -20,14 +20,7 @@ */ package jalview.ws.jws2; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentView; -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.util.Locale; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; @@ -37,11 +30,19 @@ 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; +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.params.WsParamSetI; /** * DOCUMENT ME! @@ -58,7 +59,7 @@ public class MsaWSClient extends Jws2Client public MsaWSClient(Jws2Instance 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, @@ -68,7 +69,7 @@ public class MsaWSClient extends Jws2Client public MsaWSClient(Jws2Instance 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, @@ -95,7 +96,7 @@ public class MsaWSClient extends Jws2Client public MsaWSClient(Jws2Instance 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); @@ -107,30 +108,30 @@ public class MsaWSClient extends Jws2Client if (!(sh.service instanceof MsaWS)) { // 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.serviceType }), + MessageManager.getString("label.internal_jalview_error"), + JvOptionPane.WARNING_MESSAGE); return; } server = (MsaWS) sh.service; 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.serviceType }), + MessageManager.getString("label.internal_jalview_error"), + JvOptionPane.WARNING_MESSAGE); return; } startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset); - } public MsaWSClient() @@ -140,7 +141,7 @@ 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()) // { @@ -149,12 +150,11 @@ public class MsaWSClient extends Jws2Client wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") + " of " + altitle + "\nJob details\n"); - String jobtitle = WebServiceName.toLowerCase(); + String jobtitle = WebServiceName.toLowerCase(Locale.ROOT); 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 " @@ -171,9 +171,9 @@ public class MsaWSClient extends Jws2Client + "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); @@ -182,21 +182,14 @@ public class MsaWSClient extends Jws2Client } 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"; @@ -220,10 +213,11 @@ public class MsaWSClient extends Jws2Client return (WebServiceName.indexOf("lustal") > -1); // cheat! } + @Override public void attachWSMenuEntry(JMenu rmsawsmenu, - final Jws2Instance service, final AlignFrame alignFrame) + final Jws2Instance service, final AlignFrame af) { - if (registerAAConWSInstance(rmsawsmenu, service, alignFrame)) + if (registerAAConWSInstance(rmsawsmenu, service, af)) { // Alignment dependent analysis calculation WS gui return; @@ -250,8 +244,8 @@ public class MsaWSClient extends Jws2Client 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")); @@ -268,15 +262,17 @@ public class MsaWSClient extends Jws2Client method.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - AlignmentView msa = alignFrame.gatherSequencesForAlignment(); + AlignmentView msa = af.gatherSequencesForAlignment(); if (msa != null) { - new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps, - true, alignFrame.getViewport().getAlignment() - .getDataset(), alignFrame); + new MsaWSClient(service, af.getTitle(), msa, withGaps, + true, + af.getViewport().getAlignment().getDataset(), + af); } } @@ -288,19 +284,18 @@ 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(); + AlignmentView msa = af.gatherSequencesForAlignment(); if (msa != null) { - new MsaWSClient(service, null, null, true, alignFrame - .getTitle(), msa, withGaps, true, alignFrame - .getViewport().getAlignment().getDataset(), alignFrame); + startJob(service, af, withGaps, msa); } } @@ -315,9 +310,9 @@ public class MsaWSClient extends Jws2Client final int showToolTipFor = ToolTipManager.sharedInstance() .getDismissDelay(); - for (final WsParamSetI preset : presets) + for (final WsParamSetI preSet : presets) { - final JMenuItem methodR = new JMenuItem(preset.getName()); + final JMenuItem methodR = new JMenuItem(preSet.getName()); final int QUICK_TOOLTIP = 1500; // JAL-1582 shorten tooltip display time in these menu items as // they can obscure other options @@ -326,39 +321,40 @@ 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 + AlignmentView msa = af .gatherSequencesForAlignment(); if (msa != null) { - MsaWSClient msac = new MsaWSClient(service, preset, - alignFrame.getTitle(), - msa, false, true, alignFrame.getViewport() - .getAlignment().getDataset(), alignFrame); + MsaWSClient msac = new MsaWSClient(service, preSet, + af.getTitle(), msa, false, true, + af.getViewport().getAlignment() + .getDataset(), + af); } } @@ -380,4 +376,20 @@ public class MsaWSClient extends Jws2Client } } while (!finished); } + + protected void startJob(final Jws2Instance service, final AlignFrame af, + final boolean withGaps, AlignmentView msa) + { + try { + new MsaWSClient(service, null, null, true, + af.getTitle(), msa, withGaps, true, + af.getViewport().getAlignment().getDataset(), + af); + } catch (Exception e) { + JvOptionPane.showMessageDialog(alignFrame, e.getMessage(), + MessageManager.getString("label.state_job_error"), + JvOptionPane.WARNING_MESSAGE); + + } + } }