JAL-2505 JAL-2542 SequenceFeatures.shift() to shift all positional

[jalview.git] / src / jalview / datamodel / features / SequenceFeaturesI.java

diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
index cfcdc76..58beca2 100644 (file)
--- a/src/jalview/datamodel/features/SequenceFeaturesI.java
+++ b/src/jalview/datamodel/features/SequenceFeaturesI.java
@@ -33,8 +33,12 @@ public interface SequenceFeaturesI
           String... type);
 
   /**
-   * Answers a list of all features stored, optionally restricted to specified
-   * types, in no particular guaranteed order
+   * Answers a list of all features stored, in no particular guaranteed order.
+   * Positional features may optionally be restricted to specified types, but
+   * all non-positional features (if any) are always returned.
+   * <p>
+   * To filter non-positional features by type, use
+   * getNonPositionalFeatures(type).
    * 
    * @param type
    * @return
@@ -42,6 +46,32 @@ public interface SequenceFeaturesI
   List<SequenceFeature> getAllFeatures(String... type);
 
   /**
+   * Answers a list of all positional (or non-positional) features which are in
+   * the specified feature group, optionally restricted to features of specified
+   * types.
+   * 
+   * @param positional
+   *          if true returns positional features, else non-positional features
+   * @param group
+   *          the feature group to be matched (which may be null)
+   * @param type
+   *          optional feature types to filter by
+   * @return
+   */
+  List<SequenceFeature> getFeaturesForGroup(boolean positional,
+          String group, String... type);
+
+  /**
+   * Answers a list of all features stored, whose type either matches one of the
+   * given ontology terms, or is a specialisation of a term in the Sequence
+   * Ontology. Results are returned in no particular guaranteed order.
+   * 
+   * @param ontologyTerm
+   * @return
+   */
+  List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm);
+
+  /**
    * Answers the number of (positional or non-positional) features, optionally
    * restricted to specified feature types. Contact features are counted as 1.
    * 
@@ -134,11 +164,13 @@ public interface SequenceFeaturesI
           boolean positionalFeatures, String... groups);
 
   /**
-   * Answers a set of the distinct feature types for which a feature is stored
+   * Answers a set of the distinct feature types for which a feature is stored.
+   * The types may optionally be restricted to those which match, or are a
+   * subtype of, given sequence ontology terms
    * 
    * @return
    */
-  Set<String> getFeatureTypes();
+  Set<String> getFeatureTypes(String... soTerm);
 
   /**
    * Answers the minimum score held for positional or non-positional features
@@ -161,4 +193,12 @@ public interface SequenceFeaturesI
    * @return
    */
   float getMaximumScore(String type, boolean positional);
+
+  /**
+   * Adds the shift amount to the start and end of all positional features,
+   * returning true if at least one feature was shifted, else false
+   * 
+   * @param shift
+   */
+  abstract boolean shiftFeatures(int shift);
 }
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