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package jalview.ws.slivkaws; |
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import jalview.api.FeatureColourI; |
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import jalview.bin.Cache; |
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import jalview.bin.Console; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.SequenceI; |
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import jalview.datamodel.features.FeatureMatcherSetI; |
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import jalview.io.AnnotationFile; |
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import jalview.io.DataSourceType; |
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import jalview.io.FeaturesFile; |
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import jalview.util.MessageManager; |
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import jalview.ws.api.JobId; |
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import jalview.ws.api.SequenceAnnotationServiceI; |
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import jalview.ws.params.ArgumentI; |
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import jalview.ws.params.WsParamSetI; |
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import jalview.ws.uimodel.AlignAnalysisUIText; |
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import java.io.IOError; |
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import java.io.IOException; |
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import java.util.Arrays; |
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import java.util.Collection; |
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import java.util.List; |
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import java.util.Map; |
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import compbio.data.msa.Category; |
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import uk.ac.dundee.compbio.slivkaclient.RemoteFile; |
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import uk.ac.dundee.compbio.slivkaclient.SlivkaClient; |
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import uk.ac.dundee.compbio.slivkaclient.SlivkaService; |
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Uncovered Elements: 36 (36) |
Complexity: 11 |
Complexity Density: 0.48 |
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public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI |
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{ |
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Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
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 public SlivkaAnnotationServiceInstance(SlivkaClient client,... |
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SlivkaService service, String category) |
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{ |
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super(client, service, category); |
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if (category == Category.CATEGORY_CONSERVATION) |
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{ |
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setAlignAnalysisUI(new AlignAnalysisUIText(getName(), |
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SlivkaAnnotationServiceInstance.class, |
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"Slivka.AACons", false, true, true, true, true, 2, |
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MessageManager.getString("label.aacon_calculations"), |
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MessageManager.getString("tooltip.aacon_calculations"), |
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MessageManager.getString("label.aacon_settings"), |
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MessageManager.getString("tooltip.aacon_settings"))); |
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} |
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style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT; |
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} |
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Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable |
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{ |
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return super.submit(seqs, preset, paramset); |
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} |
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| 0% |
Uncovered Elements: 26 (26) |
Complexity: 8 |
Complexity Density: 0.44 |
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@Override... |
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public List<AlignmentAnnotation> getAnnotationResult(JobId jobId, |
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List<SequenceI> seqs, Map<String, FeatureColourI> featureColours, |
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Map<String, FeatureMatcherSetI> featureFilters) throws Throwable |
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{ |
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RemoteFile annotFile = null; |
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RemoteFile featFile = null; |
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try |
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{ |
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Collection<RemoteFile> files = client.fetchFilesList(jobId.getJobId()); |
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for (RemoteFile f : files) |
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{ |
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if (f.getMediaType().equals("application/jalview-annotations")) |
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{ |
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annotFile = f; |
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} |
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else if (f.getMediaType().equals("application/jalview-features")) |
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{ |
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featFile = f; |
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} |
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} |
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} catch (IOException e) |
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{ |
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throw new IOError(e); |
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} |
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Alignment aln = new Alignment(seqs.toArray(new SequenceI[0])); |
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if (annotFile == null |
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|| !new AnnotationFile().readAnnotationFileWithCalcId(aln, service.getId(), annotFile.getContentUrl().toString(), DataSourceType.URL)) |
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{ |
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Console.debug("No annotation from slivka job\n" + annotFile); |
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} |
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else { |
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Console.debug("Annotation file loaded " + annotFile); |
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} |
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if (featFile == null |
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|| !new FeaturesFile(featFile.getContentUrl().toString(), DataSourceType.URL).parse(aln, featureColours, true)) |
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{ |
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Console.debug("No features from slivka job\n" + featFile); |
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} |
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else { |
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Console.debug("Features feil loaded " + featFile); |
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} |
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return Arrays.asList(aln.getAlignmentAnnotation()); |
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} |
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} |
