X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesI.java;h=ca0283e71470bdfbc060a164b1a10df2eb0bc340;hb=09d3b755d9b00f5c3acb44049aedd49361dc0690;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..ca0283e 100644
--- a/src/jalview/datamodel/features/SequenceFeaturesI.java
+++ b/src/jalview/datamodel/features/SequenceFeaturesI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel.features;
import jalview.datamodel.SequenceFeature;
@@ -12,7 +32,8 @@ 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 +53,12 @@ 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 +66,32 @@ 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, or is a
+ * specialisation (in the Sequence Ontology) of, one of the given terms.
+ * Results are returned in no particular 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 +184,13 @@ 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 +213,19 @@ public interface SequenceFeaturesI
* @return
*/
float getMaximumScore(String type, boolean positional);
-}
\ No newline at end of file
+
+ /**
+ * 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);
+
+ /**
+ * Deletes all positional and non-positional features
+ */
+ void deleteAll();
+}