src/jalview/datamodel/features/SequenceFeatures.java

   1 package jalview.datamodel.features;
   2
   3 import jalview.datamodel.SequenceFeature;
   4
   5 import java.util.Collections;
   6 import java.util.HashMap;
   7 import java.util.List;
   8 import java.util.Map;
   9
  10 public class SequenceFeatures
  11 {
  12
  13   /*
  14    * map from feature type to structured store of features for that type
  15    */
  16   private Map<String, FeatureStore> featureStore;
  17
  18   /**
  19    * Constructor
  20    */
  21   public SequenceFeatures()
  22   {
  23     featureStore = new HashMap<String, FeatureStore>();
  24   }
  25
  26   /**
  27    * Add one sequence feature to the store
  28    *
  29    * @param sf
  30    */
  31   public void add(SequenceFeature sf)
  32   {
  33     String type = sf.getType();
  34     if (featureStore.get(type) == null)
  35     {
  36       featureStore.put(type, new FeatureStore());
  37     }
  38     featureStore.get(type).addFeature(sf);
  39   }
  40
  41   /**
  42    * Returns a (possibly empty) list of features of the given type which overlap
  43    * the (inclusive) sequence position range
  44    *
  45    * @param type
  46    * @param from
  47    * @param to
  48    * @return
  49    */
  50   public List<SequenceFeature> findFeatures(String type, int from,
  51           int to)
  52   {
  53     FeatureStore features = featureStore.get(type);
  54     if (features == null)
  55     {
  56       return Collections.emptyList();
  57     }
  58     return features.findOverlappingFeatures(from, to);
  59   }
  60 }