X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesI.java;h=40beae367d219f435a214abf450bb7fa97211f8c;hb=1580169b8b5b244d380ec7b99a732dd34b0d454a;hp=fa775327cb0f06844b4041e1bbb67b30e1b368ae;hpb=0a461d38627bf41323b8f77e5c6f45b300025494;p=jalview.git
diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
index fa77532..40beae3 100644
--- a/src/jalview/datamodel/features/SequenceFeaturesI.java
+++ b/src/jalview/datamodel/features/SequenceFeaturesI.java
@@ -12,7 +12,8 @@ public interface SequenceFeaturesI
* Adds one sequence feature to the store, and returns true, unless the
* feature is already contained in the store, in which case this method
* returns false. Containment is determined by SequenceFeature.equals()
- * comparison.
+ * comparison. Answers false, and does not add the feature, if feature type is
+ * null.
*
* @param sf
*/
@@ -32,8 +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.
+ *
+ * To filter non-positional features by type, use
+ * getNonPositionalFeatures(type).
*
* @param type
* @return
@@ -41,6 +46,32 @@ public interface SequenceFeaturesI
List 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 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 getFeaturesByOntology(String... ontologyTerm);
+
+ /**
* Answers the number of (positional or non-positional) features, optionally
* restricted to specified feature types. Contact features are counted as 1.
*
@@ -133,11 +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 getFeatureTypes();
+ Set getFeatureTypes(String... soTerm);
/**
* Answers the minimum score held for positional or non-positional features
@@ -160,4 +193,14 @@ public interface SequenceFeaturesI
* @return
*/
float getMaximumScore(String type, boolean positional);
+
+ /**
+ * Adds the shift amount to the start and end of all positional features whose
+ * start position is at or after fromPosition. Returns true if at least one
+ * feature was shifted, else false.
+ *
+ * @param fromPosition
+ * @param shiftBy
+ */
+ boolean shiftFeatures(int fromPosition, int shiftBy);
}
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