package jalview.ws2.operations;
-import java.io.IOException;
+import java.util.ArrayList;
import java.util.Collections;
-import java.util.HashMap;
import java.util.List;
-import java.util.concurrent.CancellationException;
import java.util.concurrent.CompletionStage;
+import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
-import jalview.bin.Cache;
+import jalview.api.AlignCalcManagerI2;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
import jalview.gui.WsJobParameters;
-import jalview.io.AnnotationFile;
import jalview.io.FeaturesFile;
-import jalview.util.MathUtils;
+import jalview.util.Format;
import jalview.util.MessageManager;
import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
import jalview.ws.params.WsParamSetI;
import jalview.ws2.MenuEntryProviderI;
import jalview.ws2.ResultSupplier;
-import jalview.ws2.WSJob;
-import jalview.ws2.WSJobStatus;
import jalview.ws2.PollingTaskExecutor;
import jalview.ws2.WebServiceI;
-import jalview.ws2.WebServiceWorkerI;
-import jalview.ws2.utils.WSJobList;
-
-import static java.lang.String.format;
+import jalview.ws2.gui.AnnotationMenuBuilder;
/**
- *
+ *
* @author mmwarowny
*
*/
final ResultSupplier<FeaturesFile> featuresSupplier;
+ boolean alignmentAnalysis = false;
+
+ boolean interactive = false;
+
+ /*
+ * Is it fine to get rid of AlignAnalysisUIText?
+ */
+
public AnnotationOperation(WebServiceI service,
ResultSupplier<List<AlignmentAnnotation>> annotSupplier,
ResultSupplier<FeaturesFile> featSupplier, String operationName)
{
return service.getName();
}
+
+ @Override
+ public String getDescription()
+ {
+ return service.getDescription();
+ }
@Override
public String getTypeName()
{
return service.getHostName();
}
+
+ @Override
+ public boolean hasParameters()
+ {
+ return service.hasParameters();
+ }
+
+ @Override
+ public ParamDatastoreI getParamStore()
+ {
+ return service.getParamStore();
+ }
@Override
public int getMinSequences()
@Override
public boolean isInteractive()
{
- return false;
+ return interactive;
}
- @Override
- public MenuEntryProviderI getMenuBuilder()
+ public void setInteractive(boolean value)
{
- return this::buildMenu;
+ this.interactive = value;
}
- protected void buildMenu(JMenu parent, AlignFrame frame)
+ @Override
+ public boolean isAlignmentAnalysis()
{
- final var calcName = service.getName();
- PollingTaskExecutor wsExecutor = frame.getViewport().getWSExecutor();
- {
- var item = new JMenuItem(MessageManager.formatMessage(
- "label.calcname_with_default_settings", calcName));
- item.addActionListener((event) -> {
- WebServiceWorkerI worker = new AnnotationWorker();
- wsExecutor.submit(worker);
- });
- parent.add(item);
- }
- if (service.hasParameters())
- {
- var item = new JMenuItem(
- MessageManager.getString("label.edit_settings_and_run"));
- item.setToolTipText(MessageManager.getString(
- "label.view_and_change_parameters_before_running_calculation"));
- item.addActionListener((event) -> {
- openEditParamsDialog(service, null, null)
- .thenAcceptAsync((arguments) -> {
- if (arguments != null)
- {
-
- }
- });
- });
- }
+ return alignmentAnalysis;
}
- private CompletionStage<List<ArgumentI>> openEditParamsDialog(
- WebServiceI service, WsParamSetI preset, List<ArgumentI> arguments)
+ public void setAlignmentAnalysis(boolean value)
{
- WsJobParameters jobParams;
- if (preset == null && arguments != null && arguments.size() > 0)
- jobParams = new WsJobParameters(service.getParamStore(), preset,
- arguments);
- else
- jobParams = new WsJobParameters(service.getParamStore(), preset,
- null);
- if (preset != null)
- {
- jobParams.setName(MessageManager.getString(
- "label.adjusting_parameters_for_calculation"));
- }
- var stage = jobParams.showRunDialog();
- return stage.thenApply((startJob) -> {
- if (startJob)
- {
- if (jobParams.getPreset() == null)
- return jobParams.getJobParams();
- else
- return jobParams.getPreset().getArguments();
- }
- else
- {
- return null;
- }
- });
+ this.alignmentAnalysis = value;
}
- private class AnnotationWorker implements WebServiceWorkerI
+ @Override
+ public boolean getFilterNonStandardSymbols()
{
- private long uid = MathUtils.getUID();
-
- private WSJobList jobs = new WSJobList();
-
- private HashMap<Long, Integer> exceptionCount = new HashMap<>();
-
- private static final int MAX_RETRY = 5;
-
- @Override
- public long getUID()
- {
- return uid;
- }
-
- @Override
- public WebServiceI getWebService()
- {
- return service;
- }
-
- @Override
- public List<WSJob> getJobs()
- {
- return Collections.unmodifiableList(jobs);
- }
-
- @Override
- public void start() throws IOException
- {
-
- }
-
- @Override
- public boolean poll() throws IOException
- {
- boolean done = true;
- for (WSJob job : getJobs())
- {
- if (!job.getStatus().isDone() && !job.getStatus().isFailed())
- {
- Cache.log.debug(format("Polling job %s", job));
- try
- {
- service.updateProgress(job);
- exceptionCount.remove(job.getUid());
- } catch (IOException e)
- {
- Cache.log.error(format("Polling job %s failed.", job), e);
- int count = exceptionCount.getOrDefault(job.getUid(),
- MAX_RETRY);
- if (--count <= 0)
- {
- job.setStatus(WSJobStatus.SERVER_ERROR);
- Cache.log.warn(format(
- "Attempts limit exceeded. Droping job %s.", job));
- }
- exceptionCount.put(job.getUid(), count);
- } catch (OutOfMemoryError e)
- {
- job.setStatus(WSJobStatus.BROKEN);
- Cache.log.error(
- format("Out of memory when retrieving job %s", job), e);
- }
- Cache.log.debug(
- format("Job %s status is %s", job, job.getStatus()));
- }
- done &= job.getStatus().isDone() || job.getStatus().isFailed();
- }
- return done;
- }
-
- @Override
- public void done()
- {
- // TODO Auto-generated method stub
+ return false;
+ }
- }
+ @Override
+ public boolean getNeedsAlignedSequences()
+ {
+ return false;
+ }
+ @Override
+ public MenuEntryProviderI getMenuBuilder()
+ {
+ return new AnnotationMenuBuilder(this);
}
+
}
git://source.jalview.org / jalview.git / blobdiff