X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=319252a08de4630d5d8f7b2a92a394bd749dbc08;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=39be45402abc399ef36df90a7d371276a58612ce;hpb=b58a17a47d215b541be4d8057eb88072c599087e;p=jalview.git diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java index 39be454..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 2.8.2) - * 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. * @@ -20,11 +20,11 @@ */ 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; @@ -38,7 +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; @@ -59,7 +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, @@ -69,7 +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, @@ -96,7 +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); @@ -108,30 +107,30 @@ 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.getDesktopPane(), + 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.getDesktopPane(), 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() @@ -141,7 +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()) // { @@ -153,9 +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 " @@ -172,59 +170,25 @@ 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); - - msathread.start(); - - } - - private boolean isValidAlignment(AlignmentView av) - { - int validSeqCount = 0; - List seqs = av.getVisibleAlignment('c').getSequences(); // .getSequences(); - if (seqs.size() < 2) + MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL, + wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps, + preserveOrder, seqdataset); + if (msathread.hasValidInput()) { - JOptionPane - .showMessageDialog( - alignFrame, - "A minimum of two sequences is required to perform this operation", - "Invalid selection", JOptionPane.INFORMATION_MESSAGE); - - return false; + wsInfo.setthisService(msathread); + wsInfo.setVisible(true); + msathread.start(); } - - for (SequenceI seq : seqs) + else { - - if (seq.getSequenceAsString().matches("(-*[a-zA-Z]-*){3}[a-zA-Z-]*")) - { - ++validSeqCount; - } - if (validSeqCount > 1) - { - return true; - } + wsInfo.setVisible(false); + JvOptionPane.showMessageDialog(alignFrame, + MessageManager.getString("info.invalid_msa_input_mininfo"), + MessageManager.getString("info.invalid_msa_notenough"), + JvOptionPane.INFORMATION_MESSAGE); } - - JOptionPane - .showMessageDialog( - alignFrame, - "All selected sequence for this job must have a minimum of \nthree non-gap character to perform this operation", - "Invalid selection", JOptionPane.INFORMATION_MESSAGE); - - return false; - } - - public static void main(String[] args) - { - System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*")); } - - protected String getServiceActionKey() { return "MsaWS"; @@ -248,6 +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) { @@ -278,8 +243,8 @@ 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")); @@ -296,15 +261,17 @@ public class MsaWSClient extends Jws2Client method.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { AlignmentView msa = alignFrame.gatherSequencesForAlignment(); - if (msa != null && isValidAlignment(msa)) + 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); } } @@ -316,20 +283,21 @@ 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 && isValidAlignment(msa)) + 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); } } @@ -355,38 +323,40 @@ 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 .gatherSequencesForAlignment(); - if (msa != null && isValidAlignment(msa)) + if (msa != null) { - new MsaWSClient(service, preset, alignFrame.getTitle(), - msa, false, true, alignFrame.getViewport() - .getAlignment().getDataset(), alignFrame); + MsaWSClient msac = new MsaWSClient(service, preset, + alignFrame.getTitle(), msa, false, true, + alignFrame.getViewport().getAlignment() + .getDataset(), + alignFrame); } }