JAL-3066 JAL-3070 AACon: pass the name of the service to the alignment analysis UI

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

diff --git a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
index 4d2c4fb..7ec7e6e 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
@@ -1,18 +1,30 @@
 package jalview.ws.slivkaws;
 
+import jalview.api.FeatureColourI;
+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.gui.AnnotationWsJob;
-import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
 
+import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
+import java.io.IOError;
+import java.io.IOException;
 import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import uk.ac.dundee.compbio.slivkaclient.FormField;
 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
@@ -22,9 +34,22 @@ import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
 
 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
 {
-  public SlivkaAnnotationServiceInstance(SlivkaClient client, SlivkaService service)
+  public SlivkaAnnotationServiceInstance(SlivkaClient client,
+          SlivkaService service, boolean conservation)
   {
-    super(client, service, "Annotations");
+    super(client, service, !conservation ? "Annotations disorder"
+            : "Alignment Conservation");
+    if (conservation)
+    {
+      setAlignAnalysisUI(new AlignAnalysisUIText(service.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
@@ -66,10 +91,37 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
   }
 
   @Override
-  public List<AlignmentAnnotation> getAlignmentAnnotation(AnnotationWsJob running,
-      SeqAnnotationServiceCalcWorker abstractJabaCalcWorker) throws Throwable
+  public List<AlignmentAnnotation> getAnnotationResult(JobId job,
+          List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
+          Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
   {
-    // TODO Auto-generated method stub
-    return null;
+    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]));
+    BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
+    new AnnotationFile().parseAnnotationFrom(aln, null, readerIn);
+    if (featFile != null)
+    {
+      new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true);
+    }
+    return Arrays.asList(aln.getAlignmentAnnotation());
   }
 }