}
@Override
- public void servicesChanged(WebServiceDiscoverer discoverer,
- Collection<? extends WebServiceI> services)
+ public void operationsChanged(WebServiceDiscoverer discoverer,
+ List<Operation> list)
{
buildWebServicesMenu();
}
if (discoverer.hasServices())
{
var builder = new WebServicesMenuBuilder();
- for (var service : discoverer.getServices())
- builder.addAllOperations(service.getOperations());
+ builder.addAllOperations(discoverer.getOperations());
builder.addSelectedHostChangeListener((name, op) -> {
menu.removeAll();
builder.buildMenu(menu, this);
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.CopyOnWriteArrayList;
+import jalview.ws2.operations.Operation;
+
public interface WebServiceDiscoverer
{
public static final int STATUS_OK = 1;
public int getStatusForUrl(String url);
- public List<WebServiceI> getServices();
+ public List<Operation> getOperations();
public boolean hasServices();
@FunctionalInterface
static interface ServiceChangeListener
{
- public void servicesChanged(WebServiceDiscoverer discoverer,
- Collection<? extends WebServiceI> services);
+ public void operationsChanged(WebServiceDiscoverer discoverer,
+ List<Operation> list);
}
List<ServiceChangeListener> serviceListeners = new CopyOnWriteArrayList<>();
serviceListeners.remove(listener);
}
- default void fireServicesChanged(List<WebServiceI> services)
+ default void fireOperationsChanged(List<Operation> list)
{
for (var listener : serviceListeners)
{
- listener.servicesChanged(this, services);
+ listener.operationsChanged(this, list);
}
}
}
public String getProviderName();
- public String getName();
+ String getName();
- public String getDescription();
+ String getDescription();
- public List<Operation> getOperations();
-
- public boolean hasParameters();
+ boolean hasParameters();
public ParamDatastoreI getParamStore();
public void updateProgress(WSJob job) throws IOException;
- // public <T> ResultSupplier<T> getResultSupplier(Class<T> type);
-
public void cancel(WSJob job) throws IOException;
/**
public class WebServiceInfoUpdater implements PropertyChangeListener
{
+ private final WebServiceWorkerI worker;
private final WebserviceInfo wsInfo;
private String outputHeader = "";
- public WebServiceInfoUpdater(WebserviceInfo wsInfo)
+ public WebServiceInfoUpdater(WebServiceWorkerI worker, WebserviceInfo wsInfo)
{
+ this.worker = worker;
this.wsInfo = wsInfo;
}
break;
}
wsInfo.setStatus(job.getJobNum(), wsInfoStatus);
+ updateWSInfoGlobalStatus();
}
private void logChanged(PropertyChangeEvent evt)
newLog.substring(oldLog.length()));
}
+
+ private void updateWSInfoGlobalStatus()
+ {
+ var jobs = worker.getJobs();
+ if (jobs.countRunning() > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+ }
+ else if (jobs.countQueuing() > 0
+ || jobs.countSubmitted() < jobs.size())
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+ }
+ else
+ {
+ if (jobs.countSuccessful() > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+ }
+ else if (jobs.countCancelled() > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
+ }
+ else if (jobs.countFailed() > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ }
+ }
}
import java.io.IOException;
import java.util.List;
+import jalview.ws2.utils.WSJobList;
+
public interface WebServiceWorkerI extends PollableTaskI
-{
+{
long getUID();
- List<WSJob> getJobs();
+ WSJobList getJobs();
void start() throws IOException;
* either normally or exceptionally.
*/
void done();
+
+ public void addListener(WebServiceWorkerListener listener);
}
--- /dev/null
+package jalview.ws2;
+
+public interface WebServiceWorkerListener
+{
+ void workerStarted(WebServiceWorkerI source);
+
+ void workerNotStarted(WebServiceWorkerI source);
+
+ void jobCreated(WebServiceWorkerI source, WSJob job);
+
+ void pollException(WebServiceWorkerI source, WSJob job, Exception e);
+
+ void workerCompleting(WebServiceWorkerI source);
+
+ void workerCompleted(WebServiceWorkerI source);
+}
--- /dev/null
+package jalview.ws2;
+
+import java.util.List;
+import java.util.concurrent.CopyOnWriteArrayList;
+import java.util.function.Consumer;
+
+public class WebServiceWorkerListenersList
+{
+ private WebServiceWorkerI owner;
+ private List<WebServiceWorkerListener> listeners = new CopyOnWriteArrayList<>();
+
+ public WebServiceWorkerListenersList(WebServiceWorkerI worker)
+ {
+ this.owner = worker;
+ }
+
+ public void addListener(WebServiceWorkerListener listener)
+ {
+ listeners.add(listener);
+ }
+
+ public void removeListener(WebServiceWorkerListener listener)
+ {
+ listeners.remove(listener);
+ }
+
+ public void fireWorkerStarted()
+ {
+ for (var listener : listeners)
+ listener.workerStarted(owner);
+ }
+
+ public void fireWorkerNotStarted()
+ {
+ for (var listener : listeners)
+ listener.workerNotStarted(owner);
+ }
+
+ public void fireJobCreated(WSJob job)
+ {
+ for (var listener : listeners)
+ listener.jobCreated(owner, job);
+ }
+
+ public void firePollException(WSJob job, Exception e)
+ {
+ for (var listener : listeners)
+ listener.pollException(owner, job, e);
+ }
+
+ public void fireWorkerCompleting()
+ {
+ for (var listener : listeners)
+ listener.workerCompleting(owner);
+ }
+
+ public void fireWorkerCompleted()
+ {
+ for (var listener : listeners)
+ listener.workerCompleted(owner);
+ }
+
+ public List<WebServiceWorkerListener> getListeners()
+ {
+ return listeners;
+ }
+
+ public void forEach(Consumer<WebServiceWorkerListener> consumer)
+ {
+ for (var listener : listeners)
+ consumer.accept(listener);
+ }
+}
--- /dev/null
+package jalview.ws2.gui;
+
+import static java.lang.String.format;
+
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Objects;
+import java.util.concurrent.CompletionStage;
+import java.util.function.Consumer;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.ToolTipManager;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.HiddenColumns;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.WebserviceInfo;
+import jalview.gui.WsJobParameters;
+import jalview.util.MathUtils;
+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.PollingTaskExecutor;
+import jalview.ws2.WSJob;
+import jalview.ws2.WebServiceInfoUpdater;
+import jalview.ws2.WebServiceWorkerI;
+import jalview.ws2.WebServiceWorkerListener;
+import jalview.ws2.operations.AlignmentOperation;
+import jalview.ws2.operations.AlignmentOperation.AlignmentResult;
+import jalview.ws2.operations.AlignmentOperation.AlignmentWorker;
+
+
+public class AlignmentMenuBuilder implements MenuEntryProviderI
+{
+ AlignmentOperation operation;
+
+ public AlignmentMenuBuilder(AlignmentOperation operation)
+ {
+ this.operation = operation;
+ }
+
+ public void buildMenu(JMenu parent, AlignFrame frame)
+ {
+ if (operation.canSubmitGaps())
+ {
+ var alignSubmenu = new JMenu(operation.getName());
+ buildMenu(alignSubmenu, frame, false);
+ parent.add(alignSubmenu);
+ var realignSubmenu = new JMenu(MessageManager.formatMessage(
+ "label.realign_with_params", operation.getName()));
+ realignSubmenu.setToolTipText(MessageManager
+ .getString("label.align_sequences_to_existing_alignment"));
+ buildMenu(realignSubmenu, frame, true);
+ parent.add(realignSubmenu);
+ }
+ else
+ {
+ buildMenu(parent, frame, false);
+ }
+ }
+
+ protected void buildMenu(JMenu parent, AlignFrame frame,
+ boolean submitGaps)
+ {
+ final String action = submitGaps ? "Align" : "Realign";
+ final var calcName = operation.getName();
+
+ {
+ var item = new JMenuItem(MessageManager.formatMessage(
+ "label.calcname_with_default_settings", calcName));
+ item.setToolTipText(MessageManager
+ .formatMessage("label.action_with_default_settings", action));
+ item.addActionListener((event) -> {
+ final AlignmentView msa = frame.gatherSequencesForAlignment();
+ if (msa != null)
+ {
+ startWorker(frame, msa, Collections.emptyList(), submitGaps);
+ }
+ });
+ parent.add(item);
+ }
+
+ if (operation.hasParameters())
+ {
+ var item = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ item.setToolTipText(MessageManager.getString(
+ "label.view_and_change_parameters_before_alignment"));
+ item.addActionListener((event) -> {
+ AlignmentView msa = frame.gatherSequencesForAlignment();
+ if (msa != null)
+ {
+ openEditParamsDialog(operation.getParamStore(), null, null)
+ .thenAcceptAsync((arguments) -> {
+ if (arguments != null)
+ {
+ startWorker(frame, msa, arguments, submitGaps);
+ }
+ });
+ }
+ });
+ parent.add(item);
+ }
+
+ var presets = operation.getParamStore().getPresets();
+ if (presets != null && presets.size() > 0)
+ {
+ final var presetList = new JMenu(MessageManager
+ .formatMessage("label.run_with_preset_params", calcName));
+ final var showToolTipFor = ToolTipManager.sharedInstance()
+ .getDismissDelay();
+ for (final var preset : presets)
+ {
+ var item = new JMenuItem(preset.getName());
+ final int QUICK_TOOLTIP = 1500;
+ item.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ ToolTipManager.sharedInstance().setDismissDelay(QUICK_TOOLTIP);
+ }
+
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
+ }
+ });
+ String tooltip = JvSwingUtils.wrapTooltip(true,
+ format("<strong>%s</strong><br/>%s",
+ MessageManager.getString(
+ preset.isModifiable() ? "label.user_preset"
+ : "label.service_preset"),
+ preset.getDescription()));
+ item.setToolTipText(tooltip);
+ item.addActionListener((event) -> {
+ AlignmentView msa = frame.gatherSequencesForAlignment();
+ startWorker(frame, msa, preset.getArguments(), submitGaps);
+ });
+ presetList.add(item);
+ }
+ parent.add(presetList);
+ }
+ }
+
+ private CompletionStage<List<ArgumentI>> openEditParamsDialog(
+ ParamDatastoreI paramStore, WsParamSetI preset,
+ List<ArgumentI> arguments)
+ {
+ WsJobParameters jobParams;
+ if (preset == null && arguments != null && arguments.size() > 0)
+ jobParams = new WsJobParameters(paramStore, preset, arguments);
+ else
+ jobParams = new WsJobParameters(paramStore, 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;
+ }
+ });
+ }
+
+ private void startWorker(AlignFrame frame, AlignmentView msa,
+ List<ArgumentI> arguments, boolean submitGaps)
+ {
+ AlignViewport viewport = frame.getViewport();
+ PollingTaskExecutor executor = frame.getViewport().getWSExecutor();
+ if (msa != null)
+ {
+
+ String panelInfo = String.format("%s using service hosted at %s%n%s",
+ operation.getName(), operation.getHostName(),
+ Objects.requireNonNullElse(operation.getDescription(), ""));
+ var wsInfo = new WebserviceInfo(operation.getName(), panelInfo, false);
+
+ final String alnTitle = frame.getTitle();
+ AlignmentWorker worker = operation.new AlignmentWorker(msa,
+ arguments, frame.getTitle(), submitGaps, true,
+ viewport);
+ String outputHeader = String.format("%s of %s%nJob details%n",
+ submitGaps ? "Re-alignment" : "Alignment", alnTitle);
+
+ var awl = new AlignmentWorkerListener(worker, wsInfo, frame,
+ outputHeader);
+ worker.setResultConsumer(awl);
+ worker.addListener(awl);
+
+ executor.submit(worker);
+ }
+
+ }
+
+ private class AlignmentWorkerListener
+ implements WebServiceWorkerListener, Consumer<AlignmentResult>
+ {
+
+ final WebServiceWorkerI worker;
+ final WebserviceInfo wsInfo;
+ final AlignFrame frame;
+ WebServiceInfoUpdater updater;
+ String outputHeader;
+ final long progbarId = MathUtils.getUID();
+
+ private AlignmentWorkerListener(WebServiceWorkerI worker, WebserviceInfo wsInfo,
+ AlignFrame frame, String header)
+ {
+ this.worker = worker;
+ this.wsInfo = wsInfo;
+ this.frame = frame;
+ this.outputHeader = header;
+ this.updater = new WebServiceInfoUpdater(worker, wsInfo);
+ updater.setOutputHeader(outputHeader);
+ }
+
+ @Override
+ public void workerStarted(WebServiceWorkerI source)
+ {
+ // wsInfo.setThisService() should happen here
+ wsInfo.setVisible(true);
+ }
+
+ @Override
+ public void workerNotStarted(WebServiceWorkerI source)
+ {
+ wsInfo.setVisible(false);
+ // TODO show notification dialog.
+ JvOptionPane.showMessageDialog(frame,
+ MessageManager.getString("info.invalid_msa_input_mininfo"),
+ MessageManager.getString("info.invalid_msa_notenough"),
+ JvOptionPane.INFORMATION_MESSAGE);
+ }
+
+ @Override
+ public void jobCreated(WebServiceWorkerI source, WSJob job)
+ {
+ int tabIndex = wsInfo.addJobPane();
+ wsInfo.setProgressName(String.format("region %d", job.getJobNum()),
+ tabIndex);
+ wsInfo.setProgressText(tabIndex, outputHeader);
+ job.addPropertyChangeListener(updater);
+ }
+
+ @Override
+ public void pollException(WebServiceWorkerI source, WSJob job, Exception e)
+ {
+ wsInfo.appendProgressText(job.getJobNum(),
+ MessageManager.formatMessage("info.server_exception",
+ operation.getName(), e.getMessage()));
+ }
+
+ @Override
+ public void workerCompleting(WebServiceWorkerI source)
+ {
+ // TODO Auto-generated method stub
+ wsInfo.setProgressBar(
+ MessageManager.getString("status.collecting_job_results"),
+ progbarId);
+ }
+
+ @Override
+ public void workerCompleted(WebServiceWorkerI source)
+ {
+ wsInfo.removeProgressBar(progbarId);
+
+ }
+
+ @Override
+ public void accept(AlignmentResult out)
+ {
+ if (out != null)
+ {
+ wsInfo.showResultsNewFrame.addActionListener(evt -> displayNewFrame(
+ new Alignment(out.getAln()), out.getAlorders(), out.getHidden()));
+ wsInfo.setResultsReady();
+ }
+ else
+ {
+ wsInfo.setFinishedNoResults();
+ }
+ }
+
+ private void displayNewFrame(AlignmentI aln,
+ List<AlignmentOrder> alorders, HiddenColumns hidden)
+ {
+ AlignFrame frame = new AlignFrame(aln, hidden,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ // TODO store feature renderer settings in worker object
+ // frame.getFeatureRenderer().transferSettings(featureSettings);
+ var regions = sortOrders(alorders);
+ if (alorders.size() == 1)
+ {
+ frame.addSortByOrderMenuItem(
+ format("%s Ordering", operation.getName()), alorders.get(0));
+ }
+ else
+ {
+ for (int i = 0; i < alorders.size(); i++)
+ {
+ final int j = i;
+ Iterable<String> iter = () -> regions.get(j).stream()
+ .map(it -> Integer.toString(it)).iterator();
+ var orderName = format("%s Region %s Ordering", operation.getName(),
+ String.join(",", iter));
+ frame.addSortByOrderMenuItem(orderName, alorders.get(i));
+ }
+ }
+
+ /* TODO
+ * If alignment was requested from one half of a SplitFrame, show in a
+ * SplitFrame with the other pane similarly aligned.
+ */
+
+ Desktop.addInternalFrame(frame, frame.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+
+ private List<List<Integer>> sortOrders(List<?> alorders)
+ {
+ List<List<Integer>> regions = new ArrayList<>();
+ for (int i = 0; i < alorders.size(); i++)
+ {
+ List<Integer> regs = new ArrayList<>();
+ regs.add(i);
+ int j = i + 1;
+ while (j < alorders.size())
+ {
+ if (alorders.get(i).equals(alorders.get(j)))
+ {
+ alorders.remove(j);
+ regs.add(j);
+ }
+ else
+ {
+ j++;
+ }
+ }
+ regions.add(regs);
+ }
+ return regions;
+ }
+
+
+ }
+}
+
--- /dev/null
+package jalview.ws2.gui;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+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.api.AlignCalcManagerI2;
+import jalview.api.AlignmentViewPanel;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.WsJobParameters;
+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.PollingTaskExecutor;
+import jalview.ws2.operations.AnnotationOperation;
+import jalview.ws2.operations.AnnotationServiceWorker;
+
+public class AnnotationMenuBuilder implements MenuEntryProviderI
+{
+ final AnnotationOperation operation;
+
+ public AnnotationMenuBuilder(AnnotationOperation operation)
+ {
+ this.operation = operation;
+ }
+
+ @Override
+ public void buildMenu(JMenu parent, AlignFrame frame)
+ {
+ if (operation.isInteractive())
+ buildInteractiveMenu(parent, frame);
+ else
+ buildClassicMenu(parent, frame);
+ }
+
+ protected void buildClassicMenu(JMenu parent, AlignFrame frame)
+ {
+ final var calcName = operation.getName();
+ PollingTaskExecutor wsExecutor = frame.getViewport().getWSExecutor();
+ final var calcManager = frame.getViewport().getCalcManager();
+ {
+ var item = new JMenuItem(MessageManager.formatMessage(
+ "label.calcname_with_default_settings", calcName));
+ item.addActionListener((event) -> {
+ var worker = createWorker(Collections.emptyList(), frame, calcManager);
+ calcManager.startWorker(worker);
+ });
+ parent.add(item);
+ }
+ if (operation.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(operation.getParamStore(), null, null)
+ .thenAcceptAsync((arguments) -> {
+ if (arguments != null)
+ {
+ var worker = createWorker(arguments, frame, calcManager);
+ calcManager.startWorker(worker);
+ }
+ });
+ });
+ parent.add(item);
+ }
+ }
+
+ protected void buildInteractiveMenu(JMenu parent, AlignFrame frame)
+ {
+ final var calcName = operation.getName();
+ final var calcManager = frame.getViewport().getCalcManager();
+ final var arguments = new ArrayList<ArgumentI>();
+ final JCheckBoxMenuItem runItem;
+ {
+ // TODO use MessageManager and set tool tip text
+ runItem = new JCheckBoxMenuItem(
+ String.format("%s calculations", calcName));
+ runItem.addActionListener((event) -> {
+ calcManager.removeWorkersForName(calcName);
+ var worker = createWorker(arguments, frame, calcManager);
+ calcManager.registerWorker(worker);
+ });
+ parent.add(runItem);
+ }
+ JMenuItem _editItem = null;
+ if (operation.hasParameters())
+ {
+ // TODO use MessageManager and set tool tip text
+ _editItem = new JMenuItem(
+ String.format("Edit %s settings", calcName));
+ _editItem.addActionListener((event) -> {
+ openEditParamsDialog(operation.getParamStore(), null, null)
+ .thenAcceptAsync((args) -> {
+ if (arguments != null)
+ {
+ arguments.clear();
+ arguments.addAll(args);
+ calcManager.removeWorkersForName(calcName);
+ var worker = createWorker(arguments, frame, calcManager);
+ calcManager.registerWorker(worker);
+ }
+ });
+ });
+ parent.add(_editItem);
+ }
+ final var editItem = _editItem;
+
+ parent.addMenuListener(new MenuListener()
+ {
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ var isNuc = frame.getViewport().getAlignment().isNucleotide();
+ var menuEnabled = (isNuc && operation.isNucleotideOperation()) ||
+ (!isNuc && operation.isProteinOperation());
+ runItem.setEnabled(menuEnabled);
+ if (editItem != null)
+ editItem.setEnabled(menuEnabled);
+ boolean currentlyRunning = calcManager.getWorkersForName(calcName).size() > 0;
+ runItem.setSelected(currentlyRunning);
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e) {}
+
+ @Override
+ public void menuCanceled(MenuEvent e) {}
+ });
+ }
+
+
+ private CompletionStage<List<ArgumentI>> openEditParamsDialog(
+ ParamDatastoreI paramStore, WsParamSetI preset,
+ List<ArgumentI> arguments)
+ {
+ WsJobParameters jobParams;
+ if (preset == null && arguments != null && arguments.size() > 0)
+ jobParams = new WsJobParameters(paramStore, preset, arguments);
+ else
+ jobParams = new WsJobParameters(paramStore, 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;
+ }
+ });
+ }
+
+
+ private AnnotationServiceWorker createWorker(
+ List<ArgumentI> arguments, AlignFrame frame, AlignCalcManagerI2 calcManager)
+ {
+ /* What is the purpose of AlignViewport and AlignmentViewPanel? */
+ AlignViewport viewport = frame.getCurrentView();
+ AlignmentViewPanel alignPanel = frame.alignPanel;
+ return new AnnotationServiceWorker(operation,
+ arguments, viewport, alignPanel, frame, frame,
+ calcManager);
+ }
+
+}
import java.util.Map;
import java.util.Objects;
import java.util.concurrent.CompletionStage;
+import java.util.function.Consumer;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.ToolTipManager;
+import org.eclipse.jetty.http.HttpGenerator.Result;
+
import jalview.analysis.AlignSeq;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.SeqsetUtils;
import jalview.util.MathUtils;
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.WebServiceI;
import jalview.ws2.WebServiceInfoUpdater;
import jalview.ws2.WebServiceWorkerI;
+import jalview.ws2.WebServiceWorkerListener;
+import jalview.ws2.WebServiceWorkerListenersList;
+import jalview.ws2.gui.AlignmentMenuBuilder;
import jalview.ws2.utils.WSJobList;
/**
*/
public class AlignmentOperation implements Operation
{
- final WebServiceI service;
+ private final WebServiceI service;
- final ResultSupplier<AlignmentI> supplier;
+ private final ResultSupplier<AlignmentI> supplier;
+
- public AlignmentOperation(WebServiceI service,
- ResultSupplier<AlignmentI> supplier)
+ public AlignmentOperation(
+ WebServiceI service,
+ ResultSupplier<AlignmentI> supplier)
{
this.service = service;
this.supplier = supplier;
{
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()
public boolean canSubmitGaps()
{
// hack copied from original jabaws code, don't blame me
- return service.getName().contains("lustal");
+ return getName().contains("lustal");
}
@Override
@Override
public MenuEntryProviderI getMenuBuilder()
{
- return this::buildMenu;
- }
-
- protected void buildMenu(JMenu parent, AlignFrame frame)
- {
- if (canSubmitGaps())
- {
- var alignSubmenu = new JMenu(service.getName());
- buildMenu(alignSubmenu, frame, false);
- parent.add(alignSubmenu);
- var realignSubmenu = new JMenu(MessageManager.formatMessage(
- "label.realign_with_params", service.getName()));
- realignSubmenu.setToolTipText(MessageManager
- .getString("label.align_sequences_to_existing_alignment"));
- buildMenu(realignSubmenu, frame, true);
- parent.add(realignSubmenu);
- }
- else
- {
- buildMenu(parent, frame, false);
- }
+ return new AlignmentMenuBuilder(this);
}
- protected void buildMenu(JMenu parent, AlignFrame frame,
- boolean submitGaps)
- {
- final String action = submitGaps ? "Align" : "Realign";
- final var calcName = service.getName();
-
- String title = frame.getTitle();
- PollingTaskExecutor executor = frame.getViewport().getWSExecutor();
- {
- var item = new JMenuItem(MessageManager.formatMessage(
- "label.calcname_with_default_settings", calcName));
- item.setToolTipText(MessageManager
- .formatMessage("label.action_with_default_settings", action));
- item.addActionListener((event) -> {
- final AlignmentView msa = frame.gatherSequencesForAlignment();
- final AlignViewport viewport = frame.getViewport();
- final AlignmentI alignment = frame.getViewport().getAlignment();
- if (msa != null)
- {
- WebServiceWorkerI worker = new AlignmentWorker(msa,
- Collections.emptyList(), title, submitGaps, true,
- alignment, viewport);
- executor.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_alignment"));
- item.addActionListener((event) -> {
- final AlignmentView msa = frame.gatherSequencesForAlignment();
- final AlignViewport viewport = frame.getViewport();
- final AlignmentI alignment = frame.getViewport().getAlignment();
- if (msa != null)
- {
- openEditParamsDialog(service, null, null)
- .thenAcceptAsync((arguments) -> {
- if (arguments != null)
- {
- WebServiceWorkerI worker = new AlignmentWorker(msa,
- arguments, title, submitGaps, true, alignment,
- viewport);
- executor.submit(worker);
- }
- });
- }
- });
- parent.add(item);
- }
-
- var presets = service.getParamStore().getPresets();
- if (presets != null && presets.size() > 0)
- {
- final var presetList = new JMenu(MessageManager
- .formatMessage("label.run_with_preset_params", calcName));
- final var showToolTipFor = ToolTipManager.sharedInstance()
- .getDismissDelay();
- for (final var preset : presets)
- {
- var item = new JMenuItem(preset.getName());
- final int QUICK_TOOLTIP = 1500;
- item.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mouseEntered(MouseEvent e)
- {
- ToolTipManager.sharedInstance().setDismissDelay(QUICK_TOOLTIP);
- }
-
- @Override
- public void mouseExited(MouseEvent e)
- {
- ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
- }
- });
- String tooltip = JvSwingUtils.wrapTooltip(true,
- format("<strong>%s</strong><br/>%s",
- MessageManager.getString(
- preset.isModifiable() ? "label.user_preset"
- : "label.service_preset"),
- preset.getDescription()));
- item.setToolTipText(tooltip);
- item.addActionListener((event) -> {
- final AlignmentView msa = frame.gatherSequencesForAlignment();
- final AlignViewport viewport = frame.getViewport();
- final AlignmentI alignment = frame.getViewport().getAlignment();
- if (msa != null)
- {
- WebServiceWorkerI worker = new AlignmentWorker(msa,
- preset.getArguments(), title, submitGaps, true,
- alignment, viewport);
- executor.submit(worker);
- }
- });
- presetList.add(item);
- }
- parent.add(presetList);
- }
- }
-
- private CompletionStage<List<ArgumentI>> openEditParamsDialog(
- WebServiceI service, WsParamSetI preset,
- List<ArgumentI> arguments)
- {
- 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);
- 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;
- }
- });
- }
/**
* Implementation of the web service worker performing multiple sequence
* @author mmwarowny
*
*/
- private class AlignmentWorker implements WebServiceWorkerI
+ public class AlignmentWorker implements WebServiceWorkerI
{
private long uid = MathUtils.getUID();
private Map<Long, JobInput> inputs = new LinkedHashMap<>();
- private WebserviceInfo wsInfo;
-
private Map<Long, Integer> exceptionCount = new HashMap<>();
-
+
private final int MAX_RETRY = 5;
- AlignmentWorker(AlignmentView msa, List<ArgumentI> args,
+ public AlignmentWorker(AlignmentView msa, List<ArgumentI> args,
String alnTitle, boolean submitGaps, boolean preserveOrder,
- AlignmentI alignment, AlignViewport viewport)
+ AlignViewport viewport)
{
this.msa = msa;
- this.dataset = alignment.getDataset();
+ this.dataset = viewport.getAlignment().getDataset();
List<AlignedCodonFrame> cf = Objects.requireNonNullElse(
- alignment.getCodonFrames(), Collections.emptyList());
+ viewport.getAlignment().getCodonFrames(), Collections.emptyList());
this.codonFrame.addAll(cf);
this.args = args;
this.alnTitle = alnTitle;
this.preserveOrder = preserveOrder;
this.viewport = viewport;
this.gapCharacter = viewport.getGapCharacter();
-
- String panelInfo = String.format("%s using service hosted at %s%n%s",
- service.getName(), service.getHostName(),
- Objects.requireNonNullElse(service.getDescription(), ""));
- wsInfo = new WebserviceInfo(service.getName(), panelInfo, false);
}
@Override
}
@Override
- public List<WSJob> getJobs()
+ public WSJobList getJobs()
{
- return Collections.unmodifiableList(jobs);
+ return jobs;
}
@Override
public void start() throws IOException
{
Cache.log.info(format("Starting new %s job.", service.getName()));
- String outputHeader = String.format("%s of %s%nJob details%n",
- submitGaps ? "Re-alignment" : "Alignment", alnTitle);
SequenceI[][] conmsa = msa.getVisibleContigs('-');
if (conmsa == null)
{
return;
}
- WebServiceInfoUpdater updater = new WebServiceInfoUpdater(wsInfo);
- updater.setOutputHeader(outputHeader);
int numValid = 0;
for (int i = 0; i < conmsa.length; i++)
{
JobInput input = JobInput.create(conmsa[i], 2, submitGaps);
WSJob job = new WSJob(service.getProviderName(), service.getName(),
service.getHostName());
- job.setJobNum(wsInfo.addJobPane());
- if (conmsa.length > 1)
- {
- wsInfo.setProgressName(String.format("region %d", i),
- job.getJobNum());
- }
- wsInfo.setProgressText(job.getJobNum(), outputHeader);
- job.addPropertyChangeListener(updater);
+ job.setJobNum(i);
inputs.put(job.getUid(), input);
jobs.add(job);
+ listeners.fireJobCreated(job);
if (input.isInputValid())
{
int count;
}
if (numValid > 0)
{
- // wsInfo.setThisService() should happen here
- wsInfo.setVisible(true);
+ listeners.fireWorkerStarted();
}
else
{
- wsInfo.setVisible(false);
- // TODO show notification dialog.
- // JvOptionPane.showMessageDialog(frame,
- // MessageManager.getString("info.invalid_msa_input_mininfo"),
- // MessageManager.getString("info.invalid_msa_notenough"),
- // JvOptionPane.INFORMATION_MESSAGE);
+ listeners.fireWorkerNotStarted();
}
}
} catch (IOException e)
{
Cache.log.error(format("Polling job %s failed.", job), e);
- wsInfo.appendProgressText(job.getJobNum(),
- MessageManager.formatMessage("info.server_exception",
- service.getName(), e.getMessage()));
+ listeners.firePollException(job, e);
int count = exceptionCount.getOrDefault(job.getUid(),
MAX_RETRY);
if (--count <= 0)
}
done &= job.getStatus().isDone() || job.getStatus().isFailed();
}
- updateWSInfoGlobalStatus();
return done;
}
- private void updateWSInfoGlobalStatus()
- {
- if (jobs.countRunning() > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
- }
- else if (jobs.countQueuing() > 0
- || jobs.countSubmitted() < jobs.size())
- {
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
- }
- else
- {
- if (jobs.countSuccessful() > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
- }
- else if (jobs.countCancelled() > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
- }
- else if (jobs.countFailed() > 0)
- {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- }
- }
- }
@Override
public void done()
{
- long progbarId = MathUtils.getUID();
- wsInfo.setProgressBar(
- MessageManager.getString("status.collecting_job_results"),
- progbarId);
+ listeners.fireWorkerCompleting();
Map<Long, AlignmentI> results = new LinkedHashMap<>();
for (WSJob job : getJobs())
{
continue;
try
{
- AlignmentI alignment = supplier.getResult(job, dataset.getSequences(), viewport);
+ AlignmentI alignment = supplier.getResult(job,
+ dataset.getSequences(), viewport);
if (alignment != null)
{
results.put(job.getUid(), alignment);
}
}
}
- updateWSInfoGlobalStatus();
if (results.size() > 0)
{
- OutputWrapper out = prepareOutput(results);
- wsInfo.showResultsNewFrame.addActionListener(evt -> displayNewFrame(
- new Alignment(out.aln), out.alorders, out.hidden));
- wsInfo.setResultsReady();
+ AlignmentResult out = prepareResult(results);
+ resultConsumer.accept(out);
}
else
{
- wsInfo.setFinishedNoResults();
+ resultConsumer.accept(null);
}
- wsInfo.removeProgressBar(progbarId);
+ listeners.fireWorkerCompleted();
}
- private class OutputWrapper
- {
- AlignmentI aln;
-
- List<AlignmentOrder> alorders;
-
- HiddenColumns hidden;
-
- OutputWrapper(AlignmentI aln, List<AlignmentOrder> alorders,
- HiddenColumns hidden)
- {
- this.aln = aln;
- this.alorders = alorders;
- this.hidden = hidden;
- }
- }
-
- private OutputWrapper prepareOutput(Map<Long, AlignmentI> alignments)
+ private AlignmentResult prepareResult(Map<Long, AlignmentI> alignments)
{
List<AlignmentOrder> alorders = new ArrayList<>();
SequenceI[][] results = new SequenceI[jobs.size()][];
aln.setDataset(dataset);
propagateDatasetMappings(aln);
- return new OutputWrapper(aln, alorders, hidden);
+ return new AlignmentResult(aln, alorders, hidden);
// displayNewFrame(aln, alorders, hidden);
}
}
}
}
+
+ private Consumer<AlignmentResult> resultConsumer;
+
+ public void setResultConsumer(Consumer<AlignmentResult> consumer)
+ {
+ this.resultConsumer = consumer;
+ }
- private void displayNewFrame(AlignmentI aln,
- List<AlignmentOrder> alorders, HiddenColumns hidden)
+ private WebServiceWorkerListenersList listeners =
+ new WebServiceWorkerListenersList(this);
+
+ @Override
+ public void addListener(WebServiceWorkerListener listener)
{
- AlignFrame frame = new AlignFrame(aln, hidden,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- // TODO store feature renderer settings in worker object
- // frame.getFeatureRenderer().transferSettings(featureSettings);
- var regions = sortOrders(alorders);
- if (alorders.size() == 1)
- {
- frame.addSortByOrderMenuItem(
- format("%s Ordering", service.getName()), alorders.get(0));
- }
- else
- {
- for (int i = 0; i < alorders.size(); i++)
- {
- final int j = i;
- Iterable<String> iter = () -> regions.get(j).stream()
- .map(it -> Integer.toString(it)).iterator();
- var orderName = format("%s Region %s Ordering", service.getName(),
- String.join(",", iter));
- frame.addSortByOrderMenuItem(orderName, alorders.get(i));
- }
- }
+ listeners.addListener(listener);
+ }
+ }
+
+ public class AlignmentResult
+ {
+ AlignmentI aln;
- /* TODO
- * If alignment was requested from one half of a SplitFrame, show in a
- * SplitFrame with the other pane similarly aligned.
- */
+ List<AlignmentOrder> alorders;
- Desktop.addInternalFrame(frame, alnTitle, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ HiddenColumns hidden;
+
+ AlignmentResult(AlignmentI aln, List<AlignmentOrder> alorders,
+ HiddenColumns hidden)
+ {
+ this.aln = aln;
+ this.alorders = alorders;
+ this.hidden = hidden;
}
- private List<List<Integer>> sortOrders(List<?> alorders)
+ public AlignmentI getAln()
{
- List<List<Integer>> regions = new ArrayList<>();
- for (int i = 0; i < alorders.size(); i++)
- {
- List<Integer> regs = new ArrayList<>();
- regs.add(i);
- int j = i + 1;
- while (j < alorders.size())
- {
- if (alorders.get(i).equals(alorders.get(j)))
- {
- alorders.remove(j);
- regs.add(j);
- }
- else
- {
- j++;
- }
- }
- regions.add(regs);
- }
- return regions;
+ return aln;
+ }
+
+ public List<AlignmentOrder> getAlorders()
+ {
+ return alorders;
+ }
+
+ public HiddenColumns getHidden()
+ {
+ return hidden;
}
}
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.PollingTaskExecutor;
import jalview.ws2.WebServiceI;
+import jalview.ws2.gui.AnnotationMenuBuilder;
/**
*
{
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 MenuEntryProviderI getMenuBuilder()
{
- if (isInteractive())
- return this::buildInteractiveMenu;
- else
- return this::buildClassicMenu;
- }
-
- protected void buildClassicMenu(JMenu parent, AlignFrame frame)
- {
- final var calcName = service.getName();
- PollingTaskExecutor wsExecutor = frame.getViewport().getWSExecutor();
- final var calcManager = frame.getViewport().getCalcManager();
- {
- var item = new JMenuItem(MessageManager.formatMessage(
- "label.calcname_with_default_settings", calcName));
- item.addActionListener((event) -> {
- var worker = createWorker(Collections.emptyList(), frame, calcManager);
- calcManager.startWorker(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)
- {
- var worker = createWorker(arguments, frame, calcManager);
- calcManager.startWorker(worker);
- }
- });
- });
- parent.add(item);
- }
- }
-
- protected void buildInteractiveMenu(JMenu parent, AlignFrame frame)
- {
- final var calcName = service.getName();
- final var calcManager = frame.getViewport().getCalcManager();
- final var arguments = new ArrayList<ArgumentI>();
- final JCheckBoxMenuItem runItem;
- {
- // TODO use MessageManager and set tool tip text
- runItem = new JCheckBoxMenuItem(
- String.format("%s calculations", calcName));
- runItem.addActionListener((event) -> {
- calcManager.removeWorkersForName(calcName);
- var worker = createWorker(arguments, frame, calcManager);
- calcManager.registerWorker(worker);
- });
- parent.add(runItem);
- }
- JMenuItem _editItem = null;
- if (service.hasParameters())
- {
- // TODO use MessageManager and set tool tip text
- _editItem = new JMenuItem(
- String.format("Edit %s settings", calcName));
- _editItem.addActionListener((event) -> {
- openEditParamsDialog(service, null, null)
- .thenAcceptAsync((args) -> {
- if (arguments != null)
- {
- arguments.clear();
- arguments.addAll(args);
- calcManager.removeWorkersForName(calcName);
- var worker = createWorker(arguments, frame, calcManager);
- calcManager.registerWorker(worker);
- }
- });
- });
- parent.add(_editItem);
- }
- final var editItem = _editItem;
-
- parent.addMenuListener(new MenuListener()
- {
- @Override
- public void menuSelected(MenuEvent e)
- {
- var isNuc = frame.getViewport().getAlignment().isNucleotide();
- var menuEnabled = (isNuc && isNucleotideOperation()) ||
- (!isNuc && isProteinOperation());
- runItem.setEnabled(menuEnabled);
- if (editItem != null)
- editItem.setEnabled(menuEnabled);
- boolean currentlyRunning = calcManager.getWorkersForName(calcName).size() > 0;
- runItem.setSelected(currentlyRunning);
- }
-
- @Override
- public void menuDeselected(MenuEvent e) {}
-
- @Override
- public void menuCanceled(MenuEvent e) {}
- });
+ return new AnnotationMenuBuilder(this);
}
- private AnnotationServiceWorker createWorker(
- List<ArgumentI> arguments, AlignFrame frame, AlignCalcManagerI2 calcManager)
- {
- /* What is the purpose of AlignViewport and AlignmentViewPanel? */
- AlignViewport viewport = frame.getCurrentView();
- AlignmentViewPanel alignPanel = frame.alignPanel;
- return new AnnotationServiceWorker(this, service,
- arguments, viewport, alignPanel, frame, frame,
- calcManager);
- }
private CompletionStage<List<ArgumentI>> openEditParamsDialog(
WebServiceI service, WsParamSetI preset, List<ArgumentI> arguments)
private int exceptionCount = MAX_RETRY;
private static final int MAX_RETRY = 5;
- AnnotationServiceWorker(AnnotationOperation operation, WebServiceI service,
+ public AnnotationServiceWorker(AnnotationOperation operation,
List<ArgumentI> args, AlignViewport viewport, AlignmentViewPanel alignPanel,
- IProgressIndicator progressIndicator, AlignFrame frame, AlignCalcManagerI2 calcMan)
+ IProgressIndicator progressIndicator, AlignFrame frame,
+ AlignCalcManagerI2 calcMan)
{
this.operation = operation;
- this.service = service;
+ this.service = operation.service;
this.args = args;
this.viewport = viewport;
this.alignPanel = alignPanel;
package jalview.ws2.operations;
+import jalview.ws.params.ParamDatastoreI;
import jalview.ws2.MenuEntryProviderI;
public interface Operation
{
public String getName();
+
+ public String getDescription();
public String getTypeName();
public String getHostName();
+
+ public boolean hasParameters();
+
+ public ParamDatastoreI getParamStore();
public int getMinSequences();
public boolean getFilterNonStandardSymbols();
public boolean getNeedsAlignedSequences();
+
}
private static SlivkaWSDiscoverer instance = null;
- private List<WebServiceI> services = List.of();
+ private List<Operation> operations = List.of();
private SlivkaWSDiscoverer()
{
}
}
- public List<WebServiceI> getServices()
+ @Override
+ public List<Operation> getOperations()
{
- return Collections.unmodifiableList(services);
+ return Collections.unmodifiableList(operations);
}
+ @Override
public boolean hasServices()
{
- return !isRunning() && services.size() > 0;
+ return !isRunning() && operations.size() > 0;
}
public boolean isRunning()
reloadServices();
return SlivkaWSDiscoverer.this;
});
- task.thenRun(() -> fireServicesChanged(getServices()));
+ task.thenRun(() -> fireOperationsChanged(getOperations()));
discoveryTasks.add(task);
return task;
}
- private List<WebServiceI> reloadServices()
+ private List<Operation> reloadServices()
{
Cache.log.info("Reloading Slivka services");
- fireServicesChanged(Collections.emptyList());
- ArrayList<WebServiceI> allServices = new ArrayList<>();
+ fireOperationsChanged(Collections.emptyList());
+ ArrayList<Operation> allOperations= new ArrayList<>();
for (String url : getUrls())
{
SlivkaClient client = new SlivkaClient(url);
for (SlivkaService service : services)
{
SlivkaWebService instance = new SlivkaWebService(client, service);
+ Operation op = null;
for (String classifier : service.classifiers)
{
String[] path = classifier.split("\\s*::\\s*");
if (path.length >= 3 && path[0].toLowerCase().equals("operation")
&& path[1].toLowerCase().equals("analysis"))
{
- Operation op = null;
switch (path[path.length - 1].toLowerCase())
{
case "sequence alignment analysis (conservation)":
AnnotationOperation anop;
op = anop = new AnnotationOperation(instance,
- instance::getAnnotations, instance::getFeaturesFile, "Conservation");
+ instance::getAnnotations, instance::getFeaturesFile,
+ "Conservation");
anop.setAlignmentAnalysis(true);
anop.setInteractive(true);
break;
}
if (op != null)
{
- instance.addOperation(op);
break;
}
}
}
- if (instance.operations.size() > 0)
- {
- allServices.add(instance);
+ if (op != null) {
+ allOperations.add(op);
}
}
}
- this.services = allServices;
+ this.operations = allOperations;
Cache.log.info("Reloading slivka services finished");
- return allServices;
+ return allOperations;
}
@Override
protected final SlivkaClient client;
protected final SlivkaService service;
-
- protected SlivkaDatastore store = null;
-
- protected final ArrayList<Operation> operations = new ArrayList<>();
-
- protected int typeFlags = 0;
+
+ protected ParamDatastoreI store;
protected static final EnumMap<Job.Status, WSJobStatus> statusMap = new EnumMap<>(
Job.Status.class);
}
@Override
- public List<Operation> getOperations()
- {
- return operations;
- }
-
- void addOperation(Operation operation)
- {
- operations.add(operation);
- }
-
- void removeOperation(Operation operation)
- {
- operations.remove(operation);
- }
-
- @Override
public boolean hasParameters()
{
return getParamStore().getServiceParameters().size() > 0;
git://source.jalview.org / jalview.git / commitdiff