1 package jalview.ws2.gui;
3 import java.util.ArrayList;
4 import java.util.Arrays;
5 import java.util.BitSet;
6 import java.util.HashMap;
7 import java.util.LinkedHashMap;
8 import java.util.LinkedList;
11 import javax.swing.JInternalFrame;
12 import javax.swing.SwingUtilities;
14 import jalview.bin.Cache;
15 import jalview.bin.Console;
16 import jalview.datamodel.Alignment;
17 import jalview.datamodel.AlignmentI;
18 import jalview.datamodel.AlignmentOrder;
19 import jalview.datamodel.HiddenColumns;
20 import jalview.gui.AlignFrame;
21 import jalview.gui.Desktop;
22 import jalview.gui.JvOptionPane;
23 import jalview.gui.SplitFrame;
24 import jalview.gui.WebserviceInfo;
25 import jalview.util.ArrayUtils;
26 import jalview.util.MessageManager;
27 import jalview.util.Pair;
28 import jalview.ws2.actions.alignment.AlignmentAction;
29 import jalview.ws2.actions.alignment.AlignmentResult;
30 import jalview.ws2.actions.api.JobI;
31 import jalview.ws2.actions.api.TaskEventListener;
32 import jalview.ws2.actions.api.TaskI;
33 import jalview.ws2.api.JobStatus;
34 import jalview.ws2.api.WebService;
35 import jalview.ws2.helpers.WSClientTaskWrapper;
37 class AlignmentServiceGuiHandler
38 implements TaskEventListener<AlignmentResult>
40 private final WebService<?> service;
42 private final AlignFrame frame;
44 private WebserviceInfo infoPanel;
46 private String alnTitle; // title of the alignment used in new window
48 private JobI[] jobs = new JobI[0];
50 private int[] tabs = new int[0];
52 private int[] logOffset = new int[0];
54 private int[] errLogOffset = new int[0];
56 public AlignmentServiceGuiHandler(AlignmentAction action, AlignFrame frame)
58 this.service = action.getWebService();
60 String panelInfo = String.format("%s using service hosted at %s%n%s",
61 service.getName(), service.getUrl(), service.getDescription());
62 infoPanel = new WebserviceInfo(service.getName(), panelInfo, false);
63 String actionName = action.getName() != null ? action.getName() : "Alignment";
64 alnTitle = String.format("%s %s of %s", service.getName(), actionName,
69 public void taskStatusChanged(TaskI<AlignmentResult> source, JobStatus status)
74 infoPanel.setVisible(false);
75 JvOptionPane.showMessageDialog(frame,
76 MessageManager.getString("info.invalid_msa_input_mininfo"),
77 MessageManager.getString("info.invalid_msa_notenough"),
78 JvOptionPane.INFORMATION_MESSAGE);
81 infoPanel.setthisService(new WSClientTaskWrapper(source));
82 infoPanel.setVisible(true);
83 // intentional no break
86 infoPanel.setStatus(WebserviceInfo.STATE_QUEUING);
89 case UNKNOWN: // unsure what to do with unknown
90 infoPanel.setStatus(WebserviceInfo.STATE_RUNNING);
93 infoPanel.setProgressBar(
94 MessageManager.getString("status.collecting_job_results"),
95 jobs[0].getInternalId());
96 infoPanel.setStatus(WebserviceInfo.STATE_STOPPED_OK);
99 infoPanel.removeProgressBar(jobs[0].getInternalId());
100 infoPanel.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
103 infoPanel.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
106 infoPanel.removeProgressBar(jobs[0].getInternalId());
107 infoPanel.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
113 public void taskStarted(TaskI<AlignmentResult> source, List<? extends JobI> subJobs)
115 jobs = subJobs.toArray(new JobI[0]);
116 tabs = new int[subJobs.size()];
117 logOffset = new int[subJobs.size()];
118 errLogOffset = new int[subJobs.size()];
119 for (int i = 0; i < subJobs.size(); i++)
122 int tabIndex = infoPanel.addJobPane();
124 infoPanel.setProgressName(String.format("region %d", i), tabIndex);
125 infoPanel.setProgressText(tabIndex, alnTitle + "\nJob details\n");
126 // jobs should not have states other than invalid or ready at this point
127 if (job.getStatus() == JobStatus.INVALID)
128 infoPanel.setStatus(tabIndex, WebserviceInfo.STATE_STOPPED_OK);
129 else if (job.getStatus() == JobStatus.READY)
130 infoPanel.setStatus(tabIndex, WebserviceInfo.STATE_QUEUING);
135 public void taskCompleted(TaskI<AlignmentResult> source, AlignmentResult result)
137 SwingUtilities.invokeLater(() -> infoPanel.removeProgressBar(jobs[0].getInternalId()));
140 SwingUtilities.invokeLater(infoPanel::setFinishedNoResults);
143 infoPanel.showResultsNewFrame.addActionListener(evt -> {
144 var aln = result.getAlignment();
145 // copy alignment for each frame to have its own isntance
146 var alnCpy = new Alignment(aln);
147 alnCpy.setGapCharacter(aln.getGapCharacter());
148 alnCpy.setDataset(aln.getDataset());
149 displayResultsNewFrame(alnCpy, result.getAlignmentOrders(),
150 result.getHiddenColumns());
152 SwingUtilities.invokeLater(infoPanel::setResultsReady);
155 private void displayResultsNewFrame(Alignment aln,
156 List<AlignmentOrder> alorders, HiddenColumns hidden)
158 AlignFrame newFrame = new AlignFrame(aln, hidden, AlignFrame.DEFAULT_WIDTH,
159 AlignFrame.DEFAULT_HEIGHT);
160 newFrame.getFeatureRenderer().transferSettings(
161 frame.getFeatureRenderer().getSettings());
162 if (alorders.size() > 0)
164 addSortByMenuItems(newFrame, alorders);
167 var requestingFrame = frame;
168 var splitContainer = requestingFrame.getSplitViewContainer();
169 if (splitContainer != null && splitContainer.getComplement(requestingFrame) != null)
171 AlignmentI complement = splitContainer.getComplement(requestingFrame);
172 String complementTitle = splitContainer.getComplementTitle(requestingFrame);
173 Alignment copyComplement = new Alignment(complement);
174 copyComplement.setGapCharacter(complement.getGapCharacter());
175 copyComplement.setDataset(complement.getDataset());
176 copyComplement.alignAs(aln);
177 if (copyComplement.getHeight() > 0)
179 newFrame.setTitle(alnTitle);
180 AlignFrame newFrame2 = new AlignFrame(copyComplement,
181 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
182 newFrame2.setTitle(complementTitle);
183 String linkedTitle = MessageManager.getString("label.linked_view_title");
184 JInternalFrame splitFrame = new SplitFrame(
185 aln.isNucleotide() ? newFrame : newFrame2,
186 aln.isNucleotide() ? newFrame2 : newFrame);
187 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
191 // no split frame or failed to create complementary alignment
192 Desktop.addInternalFrame(newFrame, alnTitle, AlignFrame.DEFAULT_WIDTH,
193 AlignFrame.DEFAULT_HEIGHT);
196 private void addSortByMenuItems(AlignFrame frame, List<AlignmentOrder> alorders)
198 if (alorders.size() == 1)
200 frame.addSortByOrderMenuItem(service.getName() + " Ordering",
204 BitSet collected = new BitSet(alorders.size());
205 for (int i = 0, N = alorders.size(); i < N; i++)
207 if (collected.get(i))
209 var regions = new ArrayList<String>();
210 var order = alorders.get(i);
211 for (int j = i; j < N; j++)
213 if (!collected.get(j) && alorders.get(j).equals(order))
215 regions.add(Integer.toString(j + 1));
219 var orderName = String.format("%s Region %s Ordering",
220 service.getName(), String.join(",", regions));
221 frame.addSortByOrderMenuItem(orderName, order);
226 public void taskException(TaskI<AlignmentResult> source, Exception e)
228 Console.error(String.format("Service %s raised an exception.", service.getName()), e);
229 infoPanel.appendProgressText(e.getMessage());
233 public void taskRestarted(TaskI<AlignmentResult> source)
235 // alignment services are not restartable
239 public void subJobStatusChanged(TaskI<AlignmentResult> source, JobI job, JobStatus status)
241 int i = ArrayUtils.indexOf(jobs, job);
242 assert i >= 0 : "job does not exist";
244 // safeguard that should not happen irl
251 wsStatus = WebserviceInfo.STATE_STOPPED_OK;
256 wsStatus = WebserviceInfo.STATE_QUEUING;
260 wsStatus = WebserviceInfo.STATE_RUNNING;
263 wsStatus = WebserviceInfo.STATE_STOPPED_ERROR;
266 wsStatus = WebserviceInfo.STATE_CANCELLED_OK;
269 wsStatus = WebserviceInfo.STATE_STOPPED_SERVERERROR;
272 throw new AssertionError("Non-exhaustive switch statement");
274 infoPanel.setStatus(tabs[i], wsStatus);
278 public void subJobLogChanged(TaskI<AlignmentResult> source, JobI job, String log)
280 int i = ArrayUtils.indexOf(jobs, job);
281 assert i >= 0 : "job does not exist";
283 // safeguard that should never happen
285 infoPanel.appendProgressText(tabs[i], log.substring(logOffset[i]));
289 public void subJobErrorLogChanged(TaskI<AlignmentResult> source, JobI job, String log)
291 int i = ArrayUtils.indexOf(jobs, job);
292 assert i >= 0 : "job does not exist";
294 // safeguard that should never happen
296 infoPanel.appendProgressText(tabs[i], log.substring(errLogOffset[i]));