X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=8fa118dfa351f1a3db3611495e4c0607548448aa;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=66ef9a64d926c60880a9c77f39f83ecc707b7278;hpb=c9df7697dacf668e97290c57d4d117ac8cc40bc8;p=jalview.git diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java index 66ef9a6..8fa118d 100644 --- a/src/jalview/ws/jws2/MsaWSClient.java +++ b/src/jalview/ws/jws2/MsaWSClient.java @@ -1,39 +1,47 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.ws.jws2; +import jalview.datamodel.AlignmentI; +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.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.util.ArrayList; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; import java.util.List; -import javax.swing.*; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.ToolTipManager; -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.dm.JabaWsParamSet; -import jalview.ws.jws2.jabaws2.Jws2Instance; -import jalview.ws.params.WsParamSetI; /** * DOCUMENT ME! @@ -50,7 +58,7 @@ 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, @@ -58,9 +66,9 @@ public class MsaWSClient extends Jws2Client // TODO Auto-generated constructor stub } - public MsaWSClient(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, AlignmentI seqdataset, AlignFrame _alignFrame) { this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder, @@ -87,7 +95,7 @@ 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); @@ -99,26 +107,26 @@ public class MsaWSClient extends Jws2Client 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); + JOptionPane.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); return; } 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); + JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + .formatMessage("label.msa_service_is_unknown", + new String[] { sh.serviceType }), MessageManager + .getString("label.internal_jalview_error"), + JOptionPane.WARNING_MESSAGE); return; } + startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset); } @@ -130,7 +138,7 @@ 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()) // { @@ -164,8 +172,25 @@ public class MsaWSClient extends Jws2Client MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps, preserveOrder, seqdataset); - wsInfo.setthisService(msathread); - msathread.start(); + if (msathread.hasValidInput()) + { + wsInfo.setthisService(msathread); + wsInfo.setVisible(true); + msathread.start(); + } + else + { + JOptionPane.showMessageDialog(alignFrame, + MessageManager.getString("info.invalid_msa_input_mininfo"), + MessageManager.getString("info.invalid_msa_notenough"), + JOptionPane.INFORMATION_MESSAGE); + wsInfo.setVisible(false); + } + } + + public static void main(String[] args) + { + System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*")); } protected String getServiceActionKey() @@ -191,10 +216,15 @@ public class MsaWSClient extends Jws2Client return (WebServiceName.indexOf("lustal") > -1); // cheat! } - + @Override 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; @@ -217,24 +247,34 @@ public class MsaWSClient extends Jws2Client if (submitGaps == true) { action = "Realign "; - msawsmenu = new JMenu("Realign with " + svcname); - msawsmenu - .setToolTipText("Align sequences to an existing alignment"); + 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 + "with Defaults"); - method.setToolTipText(action + "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() { + @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); + } } }); @@ -243,17 +283,24 @@ public class MsaWSClient extends Jws2Client { // 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 = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + 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); + } } }); @@ -261,25 +308,62 @@ public class MsaWSClient extends Jws2Client List presets = service.getParamStore().getPresets(); if (presets != null && presets.size() > 0) { - JMenu presetlist = new JMenu("Run "+calcName + "with preset"); + JMenu presetlist = new JMenu( + MessageManager.formatMessage( + "label.run_with_preset_params", + new String[] { calcName })); + final int showToolTipFor = ToolTipManager.sharedInstance() + .getDismissDelay(); for (final WsParamSetI preset : presets) { final JMenuItem methodR = new JMenuItem(preset.getName()); - methodR.setToolTipText("

" - + JvSwingUtils.wrapTooltip("" - + (preset.isModifiable() ? "User Preset" - : "Service Preset") + "
" - + preset.getDescription() + "

") + ""); + final int QUICK_TOOLTIP = 1500; + // JAL-1582 shorten tooltip display time in these menu items as + // they can obscure other options + methodR.addMouseListener(new MouseAdapter() + { + @Override + public void mouseEntered(MouseEvent e) + { + ToolTipManager.sharedInstance().setDismissDelay( + QUICK_TOOLTIP); + } + + @Override + public void mouseExited(MouseEvent e) + { + ToolTipManager.sharedInstance().setDismissDelay( + showToolTipFor); + } + + }); + 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); + } }