X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=f3c385aef406f9ca198612b59d042b1f2dbd8a3f;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=7df3a98eee04e6421b32178c39456fbb5edb59c7;hpb=9bc61da27f002adc7f129f993904ff3b0a8c4eb0;p=jalview.git diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java index 7df3a98..f3c385a 100644 --- a/src/jalview/ws/jws2/MsaWSClient.java +++ b/src/jalview/ws/jws2/MsaWSClient.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * This file is part of Jalview. @@ -151,7 +151,8 @@ public class MsaWSClient extends Jws2Client { if (sh.paramStore == null) { - sh.paramStore = new JabaParamStore(sh); + sh.paramStore = new JabaParamStore(sh, + Desktop.getUserParameterStore()); } WsJobParameters jobParams = new WsJobParameters(sh, preset); if (!jobParams.showRunDialog()) @@ -270,17 +271,21 @@ public class MsaWSClient extends Jws2Client rmsawsmenu.add(msawsmenu); calcName = ""; } - + boolean hasparams = service.hasParameters(); do { + String action="Align "; if (submitGaps == true) { - msawsmenu = new JMenu("profile " + svcname); + action="Realign "; + msawsmenu = new JMenu("Realign with " + svcname); + msawsmenu.setToolTipText("Align sequences to an existing alignment"); rmsawsmenu.add(msawsmenu); } final boolean withGaps = submitGaps; + JMenuItem method = new JMenuItem(calcName + "Defaults"); - method.setToolTipText("Align with default settings"); + method.setToolTipText(action+"with default settings"); method.addActionListener(new ActionListener() { @@ -294,48 +299,54 @@ public class MsaWSClient extends Jws2Client } }); msawsmenu.add(method); - method = new JMenuItem(calcName + "Edit and run ..."); - method.setToolTipText("View and change the parameters before alignment."); - - method.addActionListener(new ActionListener() + if (hasparams) { - 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); + // only add these menu options if the service has user-modifiable arguments + method = new JMenuItem(calcName + "Edit and run ..."); + method.setToolTipText("View and change the parameters before alignment."); - } - }); - msawsmenu.add(method); - List presets = service.getParamStore().getPresets(); - if (presets != null && presets.size() > 0) - { - JMenu presetlist = new JMenu(calcName + "Presets"); + method.addActionListener(new ActionListener() + { + 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); - for (final WsParamSetI preset : presets) + } + }); + msawsmenu.add(method); + List presets = service.getParamStore().getPresets(); + if (presets != null && presets.size() > 0) { - final JMenuItem methodR = new JMenuItem(preset.getName()); - methodR.setToolTipText("

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

"); - methodR.addActionListener(new ActionListener() + JMenu presetlist = new JMenu(calcName + "Presets"); + + for (final WsParamSetI preset : presets) { - public void actionPerformed(ActionEvent e) + final JMenuItem methodR = new JMenuItem(preset.getName()); + methodR.setToolTipText("

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

") + ""); + methodR.addActionListener(new ActionListener() { - AlignmentView msa = alignFrame.gatherSequencesForAlignment(); - new MsaWSClient(service, preset, alignFrame.getTitle(), msa, - false, true, alignFrame.getViewport().getAlignment() - .getDataset(), alignFrame); + public void actionPerformed(ActionEvent e) + { + AlignmentView msa = alignFrame + .gatherSequencesForAlignment(); + new MsaWSClient(service, preset, alignFrame.getTitle(), + msa, false, true, alignFrame.getViewport() + .getAlignment().getDataset(), alignFrame); - } + } - }); - presetlist.add(methodR); + }); + presetlist.add(methodR); + } + msawsmenu.add(presetlist); } - msawsmenu.add(presetlist); } if (!submitGaps && canSubmitGaps()) {