src/jalview/datamodel/features/FeatureStoreI.java

   1 package jalview.datamodel.features;
   2
   3 import jalview.datamodel.SequenceFeature;
   4
   5 import java.util.Collection;
   6 import java.util.List;
   7 import java.util.Set;
   8
   9 public interface FeatureStoreI
  10 {
  11
  12   boolean addFeature(SequenceFeature feature);
  13
  14   boolean contains(SequenceFeature feature);
  15
  16   boolean delete(SequenceFeature sf);
  17
  18   List<SequenceFeature> findOverlappingFeatures(long start, long end);
  19
  20   List<SequenceFeature> findOverlappingFeatures(long start, long end,
  21           List<SequenceFeature> result);
  22
  23   List<SequenceFeature> getContactFeatures();
  24
  25   List<SequenceFeature> getContactFeatures(List<SequenceFeature> result);
  26
  27   int getFeatureCount(boolean positional);
  28
  29   Set<String> getFeatureGroups(boolean positionalFeatures);
  30
  31   Collection<SequenceFeature> getFeatures();
  32
  33   List<SequenceFeature> getFeaturesForGroup(boolean positional,
  34           String group);
  35
  36   float getMaximumScore(boolean positional);
  37
  38   float getMinimumScore(boolean positional);
  39
  40   List<SequenceFeature> getNonPositionalFeatures();
  41
  42   List<SequenceFeature> getNonPositionalFeatures(
  43           List<SequenceFeature> result);
  44
  45   List<SequenceFeature> getPositionalFeatures();
  46
  47   List<SequenceFeature> getPositionalFeatures(List<SequenceFeature> result);
  48
  49   int getTotalFeatureLength();
  50
  51   boolean isEmpty();
  52
  53   boolean shiftFeatures(int fromPosition, int shiftBy);
  54
  55   boolean listContains(List<SequenceFeature> features,
  56           SequenceFeature feature);
  57
  58 }