Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / src / jalview / ws / slivkaws / SlivkaAnnotationServiceInstance.java

diff --git a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
new file mode 100644 (file)
index 0000000..cc5c1e4
--- /dev/null
+++ b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
@@ -0,0 +1,93 @@
+package jalview.ws.slivkaws;
+
+import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.io.AnnotationFile;
+import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
+import jalview.util.MessageManager;
+import jalview.ws.api.JobId;
+import jalview.ws.api.SequenceAnnotationServiceI;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
+
+import java.io.IOError;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
+
+public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
+{
+  public SlivkaAnnotationServiceInstance(SlivkaClient client,
+          SlivkaService service, boolean conservation)
+  {
+    super(client, service, !conservation ? "Protein sequence analysis"
+        : "Alignment Conservation");
+    if (conservation)
+    {
+      setAlignAnalysisUI(new AlignAnalysisUIText(getName(),
+              SlivkaAnnotationServiceInstance.class,
+              "Slivka.AACons", false, true, true, true, true, 2,
+              MessageManager.getString("label.aacon_calculations"),
+              MessageManager.getString("tooltip.aacon_calculations"),
+              MessageManager.getString("label.aacon_settings"),
+              MessageManager.getString("tooltip.aacon_settings")));
+    }
+    style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
+  }
+
+  @Override
+  public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
+  {
+    return super.submit(seqs, preset, paramset);
+  }
+
+  @Override
+  public List<AlignmentAnnotation> getAnnotationResult(JobId job,
+          List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
+          Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
+  {
+    RemoteFile annotFile = null;
+    RemoteFile featFile = null;
+    try
+    {
+      List<RemoteFile> files = client.getJobResults(job.getJobId());
+      for (RemoteFile f : files)
+      {
+        if (f.getMimeType().equals("application/jalview-annotations"))
+        {
+          annotFile = f;
+        }
+        else if (f.getMimeType().equals("application/jalview-features"))
+        {
+          featFile = f;
+        }
+      }
+    } catch (IOException e)
+    {
+      throw new IOError(e);
+    }
+    Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
+    if (annotFile == null
+        || !new AnnotationFile().readAnnotationFile(aln, annotFile.getURL().toString(), DataSourceType.URL))
+    {
+      Cache.log.debug("No annotation from slivka job\n" + annotFile);
+    }
+    if (featFile == null
+        || !new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true))
+    {
+      Cache.log.debug("No features from slivka job\n" + featFile);
+    }
+    return Arrays.asList(aln.getAlignmentAnnotation());
+  }
+}