X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=319252a08de4630d5d8f7b2a92a394bd749dbc08;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=eee55ad1c9f4c5f48c2471356e77eeb8eac67f83;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java index eee55ad..319252a 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 2.9.0b2) - * Copyright (C) 2015 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. * @@ -20,10 +20,11 @@ */ 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; @@ -37,7 +38,6 @@ 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; @@ -58,7 +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, @@ -68,7 +68,7 @@ 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 +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); @@ -107,22 +107,24 @@ 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", - new String[] { sh.serviceType }), MessageManager - .getString("label.internal_jalview_error"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), + MessageManager.formatMessage( + "label.service_called_is_not_msa_service", + new String[] + { 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 - .formatMessage("label.msa_service_is_unknown", - new String[] { sh.serviceType }), MessageManager - .getString("label.internal_jalview_error"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager + .formatMessage("label.msa_service_is_unknown", new String[] + { sh.serviceType }), + MessageManager.getString("label.internal_jalview_error"), + JvOptionPane.WARNING_MESSAGE); return; } @@ -138,7 +140,7 @@ 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()) // { @@ -150,9 +152,8 @@ 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 " @@ -169,9 +170,9 @@ 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); @@ -180,19 +181,14 @@ 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"; @@ -216,6 +212,7 @@ public class MsaWSClient extends Jws2Client return (WebServiceName.indexOf("lustal") > -1); // cheat! } + @Override public void attachWSMenuEntry(JMenu rmsawsmenu, final Jws2Instance service, final AlignFrame alignFrame) { @@ -246,8 +243,9 @@ public class MsaWSClient extends Jws2Client if (submitGaps == true) { action = "Realign "; - msawsmenu = new JMenu(MessageManager.formatMessage( - "label.realign_with_params", new String[] { svcname })); + 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); @@ -255,14 +253,15 @@ public class MsaWSClient extends Jws2Client final boolean withGaps = submitGaps; 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 })); + "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(); @@ -270,8 +269,9 @@ public class MsaWSClient extends Jws2Client if (msa != null) { new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps, - true, alignFrame.getViewport().getAlignment() - .getDataset(), alignFrame); + true, + alignFrame.getViewport().getAlignment().getDataset(), + alignFrame); } } @@ -283,19 +283,20 @@ 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(); if (msa != null) { - new MsaWSClient(service, null, null, true, alignFrame - .getTitle(), msa, withGaps, true, alignFrame - .getViewport().getAlignment().getDataset(), + new MsaWSClient(service, null, null, true, + alignFrame.getTitle(), msa, withGaps, true, + alignFrame.getViewport().getAlignment().getDataset(), alignFrame); } @@ -305,10 +306,9 @@ public class MsaWSClient extends Jws2Client List presets = service.getParamStore().getPresets(); if (presets != null && presets.size() > 0) { - JMenu presetlist = new JMenu( - MessageManager.formatMessage( - "label.run_with_preset_params", - new String[] { calcName })); + JMenu presetlist = new JMenu(MessageManager.formatMessage( + "label.run_with_preset_params", new String[] + { calcName })); final int showToolTipFor = ToolTipManager.sharedInstance() .getDismissDelay(); @@ -323,29 +323,28 @@ 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 @@ -356,7 +355,8 @@ public class MsaWSClient extends Jws2Client MsaWSClient msac = new MsaWSClient(service, preset, alignFrame.getTitle(), msa, false, true, alignFrame.getViewport().getAlignment() - .getDataset(), alignFrame); + .getDataset(), + alignFrame); } }