From: gmungoc Date: Mon, 5 Jun 2017 07:57:27 +0000 (+0100) Subject: Merge branch 'features/JAL-2446NCList' into X-Git-Tag: Release_2_10_3b1~215 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2f219368c3a4a3ff0ed6a34f84d005a3d85c9963;p=jalview.git Merge branch 'features/JAL-2446NCList' into features/JAL-2574findFeaturesByColumn Conflicts: src/jalview/datamodel/SequenceI.java --- 2f219368c3a4a3ff0ed6a34f84d005a3d85c9963 diff --cc src/jalview/datamodel/SequenceI.java index ec76cb9,cf9d6ad..1615bee --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@@ -486,18 -511,21 +487,25 @@@ public interface SequenceI extends ASeq public List getPrimaryDBRefs(); /** - * Returns a (possibly empty) list of sequence features that overlap the range - * from-to (inclusive), optionally restricted to one or more specified feature - * types + * Returns a (possibly empty) list of sequence features that overlap the given + * alignment column range, optionally restricted to one or more specified + * feature types. If the range is all gaps, then features which enclose it are + * included (but not contact features). * - * @param from - * @param to + * @param fromCol + * start column of range inclusive (1..) + * @param toCol + * end column of range inclusive (1..) * @param types + * optional feature types to restrict results to * @return */ - List findFeatures(int from, int to, String... types); + List findFeatures(int fromCol, int toCol, String... types); + + /** + * + * @return BitSet corresponding to index [0,length) where Comparison.isGap() + * returns true. + */ + BitSet getInsertionsAsBits(); }