JAL-3070 JAL-3066 fix initialisation of slivka ServiceWithParameters

[jalview.git] / src / jalview / ws / api / SequenceAnnotationServiceI.java

diff --git a/src/jalview/ws/api/SequenceAnnotationServiceI.java b/src/jalview/ws/api/SequenceAnnotationServiceI.java
index a224bac..9ca2d31 100644 (file)
--- a/src/jalview/ws/api/SequenceAnnotationServiceI.java
+++ b/src/jalview/ws/api/SequenceAnnotationServiceI.java
@@ -1,13 +1,14 @@
 package jalview.ws.api;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
-import jalview.ws.gui.AnnotationWsJob;
-import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
 import java.util.List;
+import java.util.Map;
 
 public interface SequenceAnnotationServiceI extends JalviewWebServiceI
 {
@@ -27,14 +28,24 @@ public interface SequenceAnnotationServiceI extends JalviewWebServiceI
           List<ArgumentI> paramset) throws Throwable;
 
   /**
-   * todo: move to SequenceAnnotationResult
+   * materialise annotation and features for sequences input to the service
    * 
-   * @param running
-   * @param abstractJabaCalcWorker
-   * @return
+   * @param job
+   * @param seqs
+   *          - features and alignment annotation added to these will be
+   *          imported to the dataset for the alignment
+   * @param featureColours
+   *          - container for feature colours - any defined will be merged with
+   *          viewport
+   * @param featureFilters
+   *          - container for filters - any defined will be merged with viewport
+   * @return sequence and alignment annotation rows that should be made
+   *         visible/updated on alignment
+   * @throws Throwable
    */
-  List<AlignmentAnnotation> getAlignmentAnnotation(AnnotationWsJob running,
-          SeqAnnotationServiceCalcWorker abstractJabaCalcWorker) throws Throwable;
-
+  List<AlignmentAnnotation> getAnnotationResult(JobId job,
+          List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
+          Map<String, FeatureMatcherSetI> featureFilters) throws Throwable;
+  
 
 }