4 package jalview.ws.jws2;
6 import java.awt.event.ActionEvent;
7 import java.awt.event.ActionListener;
10 import javax.swing.JMenu;
11 import javax.swing.JMenuItem;
12 import javax.swing.JOptionPane;
14 import compbio.metadata.Argument;
16 import jalview.api.AlignCalcWorkerI;
17 import jalview.datamodel.AlignmentView;
18 import jalview.gui.AlignFrame;
19 import jalview.gui.Desktop;
20 import jalview.gui.JalviewDialog;
21 import jalview.gui.JvSwingUtils;
22 import jalview.ws.jws2.jabaws2.Jws2Instance;
23 import jalview.ws.params.WsParamSetI;
29 public class SequenceAnnotationWSClient extends Jws2Client
33 * initialise a client so its attachWSMenuEntry method can be called.
35 public SequenceAnnotationWSClient()
37 // TODO Auto-generated constructor stub
40 public SequenceAnnotationWSClient(final Jws2Instance sh,
41 AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
43 super(alignFrame, preset, null);
44 if (alignFrame.getViewport().getAlignment().isNucleotide())
46 JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
47 + " can only be used\nfor amino acid alignments.",
48 "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
52 if (sh.action.toLowerCase().contains("conservation"))
54 // Build an AACons style client - take alignment, return annotation for
57 List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
59 .getRegisteredWorkersOfClass(AAConsClient.class);
60 if (clnts == null || clnts.size() == 0)
62 if (!processParams(sh, editParams))
71 worker = new AAConsClient(sh, alignFrame, preset,
73 alignFrame.getViewport().getCalcManager().startWorker(worker);
78 AAConsClient worker = (AAConsClient) clnts.get(0);
81 paramset = worker.getArguments();
82 preset = worker.getPreset();
85 if (!processParams(sh, editParams, true))
87 // reinstate worker if it was blacklisted (might have happened due to
88 // invalid parameters)
89 alignFrame.getViewport().getCalcManager().workerMayRun(worker);
90 worker.updateParameters(preset, paramset);
94 if (sh.action.toLowerCase().contains("disorder"))
96 // build IUPred style client. take sequences, returns annotation per
98 if (!processParams(sh, editParams))
107 new AADisorderClient(sh, alignFrame, preset, paramset));
115 * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
116 * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
118 public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
119 final AlignFrame alignFrame)
121 boolean hasparams = service.hasParameters();
122 // Assume name ends in WS
123 String calcName = service.serviceType.substring(0,
124 service.serviceType.length() - 2);
126 JMenuItem aacons = new JMenuItem(calcName + " Defaults");
127 aacons.addActionListener(new ActionListener()
131 public void actionPerformed(ActionEvent e)
133 new SequenceAnnotationWSClient(service, alignFrame, null, false);
139 // only add these menu options if the service has user-modifiable
141 aacons = new JMenuItem("Edit settings and run ...");
142 aacons.setToolTipText("View and change parameters before running calculation");
144 aacons.addActionListener(new ActionListener()
146 public void actionPerformed(ActionEvent e)
148 new SequenceAnnotationWSClient(service, alignFrame, null, true);
152 List<WsParamSetI> presets = service.getParamStore().getPresets();
153 if (presets != null && presets.size() > 0)
155 JMenu presetlist = new JMenu("Run " + calcName + "with preset");
157 for (final WsParamSetI preset : presets)
159 final JMenuItem methodR = new JMenuItem(preset.getName());
160 methodR.setToolTipText("<html><p>"
161 + JvSwingUtils.wrapTooltip("<strong>"
162 + (preset.isModifiable() ? "User Preset"
163 : "Service Preset") + "</strong><br/>"
164 + preset.getDescription() + "</p>") + "</html>");
165 methodR.addActionListener(new ActionListener()
167 public void actionPerformed(ActionEvent e)
169 new SequenceAnnotationWSClient(service, alignFrame, preset,
174 presetlist.add(methodR);
176 wsmenu.add(presetlist);