1 package jalview.ws.api;
3 import jalview.api.FeatureColourI;
4 import jalview.datamodel.AlignmentAnnotation;
5 import jalview.datamodel.SequenceI;
6 import jalview.datamodel.features.FeatureMatcherSetI;
7 import jalview.ws.params.ArgumentI;
8 import jalview.ws.params.WsParamSetI;
10 import java.util.List;
13 public interface SequenceAnnotationServiceI extends JalviewWebServiceI
18 * submit sequences to service with no parameters, or preset or parameter set.
19 * Nb- almost the same as the 'align' method in the Msa service :)
27 JobId submitToService(List<SequenceI> seqs, WsParamSetI preset,
28 List<ArgumentI> paramset) throws Throwable;
31 * materialise annotation and features for sequences input to the service
35 * - features and alignment annotation added to these will be
36 * imported to the dataset for the alignment
37 * @param featureColours
38 * - container for feature colours - any defined will be merged with
40 * @param featureFilters
41 * - container for filters - any defined will be merged with viewport
42 * @return sequence and alignment annotation rows that should be made
43 * visible/updated on alignment
46 List<AlignmentAnnotation> getAnnotationResult(JobId job,
47 List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
48 Map<String, FeatureMatcherSetI> featureFilters) throws Throwable;