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package jalview.ws; |
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import jalview.bin.Console; |
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import jalview.datamodel.AlignedCodonFrame; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.AlignmentView; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AlignFrame; |
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import jalview.gui.WebserviceInfo; |
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import jalview.util.MessageManager; |
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import jalview.viewmodel.seqfeatures.FeatureRendererSettings; |
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import java.util.ArrayList; |
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import java.util.List; |
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| 0% |
Uncovered Elements: 141 (141) |
Complexity: 42 |
Complexity Density: 0.48 |
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public abstract class AWSThread extends Thread |
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{ |
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protected AlignmentI currentView = null; |
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protected FeatureRendererSettings featureSettings = null; |
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protected WebserviceInfo wsInfo = null; |
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protected AlignmentView input = null; |
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protected List<AlignedCodonFrame> codonframe = null; |
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protected boolean jobComplete = false; |
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protected AWsJob jobs[] = null; |
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protected String WebServiceName = null; |
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protected char defGapChar = '-'; |
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protected String OutputHeader; |
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protected String WsUrl = null; |
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private AlignFrame alignFrame; |
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| 0% |
Uncovered Elements: 62 (62) |
Complexity: 17 |
Complexity Density: 0.39 |
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@Override... |
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public void run() |
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{ |
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JobStateSummary jstate = null; |
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if (jobs == null) |
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jobComplete = true; |
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} |
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while (!jobComplete) |
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jstate = new JobStateSummary(); |
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for (int j = 0; j < jobs.length; j++) |
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{ |
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if (!jobs[j].submitted && jobs[j].hasValidInput()) |
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{ |
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StartJob(jobs[j]); |
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} |
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if (jobs[j].submitted && !jobs[j].subjobComplete) |
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{ |
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try |
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{ |
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pollJob(jobs[j]); |
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if (!jobs[j].hasResponse()) |
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{ |
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throw (new Exception( |
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"Timed out when communicating with server\nTry again later.\n")); |
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} |
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Console.debug("Job " + j + " Result state " + jobs[j].getState() |
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+ "(ServerError=" + jobs[j].isServerError() + ")"); |
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} catch (Exception ex) |
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{ |
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wsInfo.appendProgressText(jobs[j].jobnum, MessageManager |
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.formatMessage("info.server_exception", new Object[] |
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{ WebServiceName, ex.getMessage() })); |
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Console.warn(WebServiceName + " job(" + jobs[j].jobnum |
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+ ") Server exception."); |
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ex.printStackTrace(); |
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if (jobs[j].allowedServerExceptions > 0) |
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{ |
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jobs[j].allowedServerExceptions--; |
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Console.debug("Sleeping after a server exception."); |
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try |
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{ |
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Thread.sleep(5000); |
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} catch (InterruptedException ex1) |
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{ |
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} |
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} |
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else |
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{ |
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Console.warn("Dropping job " + j + " " + jobs[j].jobId); |
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jobs[j].subjobComplete = true; |
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wsInfo.setStatus(jobs[j].jobnum, |
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WebserviceInfo.STATE_STOPPED_SERVERERROR); |
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} |
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} catch (OutOfMemoryError er) |
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{ |
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jobComplete = true; |
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jobs[j].subjobComplete = true; |
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jobs[j].clearResponse(); |
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wsInfo.setStatus(jobs[j].jobnum, |
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WebserviceInfo.STATE_STOPPED_ERROR); |
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Console.error("Out of memory when retrieving Job " + j + " id:" |
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+ WsUrl + "/" + jobs[j].jobId, er); |
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new jalview.gui.OOMWarning( |
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"retrieving result for " + WebServiceName, er); |
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System.gc(); |
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} |
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} |
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jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]); |
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} |
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updateGlobalStatus(jstate); |
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if (!jobComplete) |
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{ |
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try |
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{ |
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Thread.sleep(5000); |
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} catch (InterruptedException e) |
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{ |
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Console.debug("Interrupted sleep waiting for next job poll.", e); |
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} |
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} |
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} |
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if (jobComplete && jobs != null) |
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{ |
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parseResult(); |
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} |
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else |
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{ |
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Console.debug( |
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"WebServiceJob poll loop finished with no jobs created."); |
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wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); |
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wsInfo.appendProgressText( |
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MessageManager.getString("info.no_jobs_ran")); |
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wsInfo.setFinishedNoResults(); |
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} |
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} |
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| 0% |
Uncovered Elements: 21 (21) |
Complexity: 6 |
Complexity Density: 0.55 |
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protected void updateGlobalStatus(JobStateSummary jstate)... |
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{ |
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if (jstate.running > 0) |
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{ |
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wsInfo.setStatus(WebserviceInfo.STATE_RUNNING); |
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} |
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else if (jstate.queuing > 0) |
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{ |
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wsInfo.setStatus(WebserviceInfo.STATE_QUEUING); |
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} |
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else |
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{ |
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jobComplete = true; |
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if (jstate.finished > 0) |
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{ |
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wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK); |
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} |
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else if (jstate.error > 0) |
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{ |
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wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); |
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} |
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else if (jstate.serror > 0) |
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{ |
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wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); |
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} |
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} |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public AWSThread()... |
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{ |
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super(); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public AWSThread(Runnable target)... |
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{ |
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super(target); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public AWSThread(String name)... |
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{ |
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super(name); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public AWSThread(ThreadGroup group, Runnable target)... |
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{ |
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super(group, target); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public AWSThread(ThreadGroup group, String name)... |
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{ |
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super(group, name); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public AWSThread(Runnable target, String name)... |
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{ |
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super(target, name); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public AWSThread(ThreadGroup group, Runnable target, String name)... |
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{ |
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super(group, target, name); |
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} |
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@param |
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@throws |
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public abstract void pollJob(AWsJob job) throws Exception; |
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@param |
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public abstract void StartJob(AWsJob job); |
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public abstract void parseResult(); |
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@param |
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| 0% |
Uncovered Elements: 14 (14) |
Complexity: 5 |
Complexity Density: 0.62 |
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public void propagateDatasetMappings(Alignment al)... |
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{ |
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if (codonframe != null) |
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{ |
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SequenceI[] alignment = al.getSequencesArray(); |
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for (int sq = 0; sq < alignment.length; sq++) |
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{ |
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for (AlignedCodonFrame acf : codonframe) |
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{ |
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final SequenceI seq = alignment[sq]; |
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if (acf != null && acf.involvesSequence(seq)) |
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{ |
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al.addCodonFrame(acf); |
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break; |
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} |
315 |
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} |
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} |
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} |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public AWSThread(ThreadGroup group, Runnable target, String name,... |
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long stackSize) |
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{ |
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super(group, target, name, stackSize); |
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} |
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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public char getGapChar()... |
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{ |
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return defGapChar; |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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public AWSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,... |
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AlignmentView input, String webServiceName, String wsUrl) |
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{ |
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this(alignFrame, wsinfo, input, wsUrl); |
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WebServiceName = webServiceName; |
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} |
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@param |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 17 (17) |
Complexity: 3 |
Complexity Density: 0.23 |
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0 |
public AWSThread(AlignFrame alframe, WebserviceInfo wsinfo2,... |
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AlignmentView alview, String wsurl2) |
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{ |
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super(); |
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this.alignFrame = alframe; |
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currentView = alframe.getCurrentView().getAlignment(); |
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featureSettings = alframe.getFeatureRenderer().getSettings(); |
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defGapChar = alframe.getViewport().getGapCharacter(); |
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this.wsInfo = wsinfo2; |
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this.input = alview; |
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WsUrl = wsurl2; |
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if (alframe != null) |
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{ |
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List<AlignedCodonFrame> cf = alframe.getViewport().getAlignment() |
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.getCodonFrames(); |
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if (cf != null) |
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{ |
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codonframe = new ArrayList<AlignedCodonFrame>(); |
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codonframe.addAll(cf); |
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} |
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} |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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protected AlignFrame getRequestingAlignFrame()... |
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{ |
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return this.alignFrame; |
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} |
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} |