package jalview.ws.api;

import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
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
{


  /**
   * submit sequences to service with no parameters, or preset or parameter set.
   * Nb- almost the same as the 'align' method in the Msa service :)
   * 
   * @param seqs
   * @param preset
   * @param paramset
   * @return
   * @throws Throwable
   */
  JobId submitToService(List<SequenceI> seqs, WsParamSetI preset,
          List<ArgumentI> paramset) throws Throwable;

  /**
   * materialise annotation and features for sequences input to the service
   * 
   * @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> getAnnotationResult(JobId job,
          List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
          Map<String, FeatureMatcherSetI> featureFilters) throws Throwable;
  

}