X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=c1687fe3dbe812899e70ab9d2081c91a6c6c267c;hb=e2c3b3602486cee3f85dd8dfc7856a5ce6701669;hp=0f78bdb4f1fd6341b6d011d4e4fb8063a5a2909d;hpb=0e65ec37e2c956e0ad94feda6fd07b7c3a9003ee;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 0f78bdb..c1687fe 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -22,6 +22,7 @@ package jalview.datamodel; import jalview.datamodel.features.SequenceFeaturesI; +import java.util.BitSet; import java.util.List; import java.util.Vector; @@ -118,9 +119,9 @@ public interface SequenceI extends ASequenceI public String getSequenceAsString(int start, int end); /** - * Get the sequence as a character array + * Answers a copy of the sequence as a character array * - * @return seqeunce and any gaps + * @return */ public char[] getSequence(); @@ -202,28 +203,14 @@ public interface SequenceI extends ASequenceI public int findPosition(int i); /** - * Returns the range of sequence positions included in the given alignment - * position range. If no positions are included (the range is entirely gaps), - * then returns null. - * - *
- * Example: - * >Seq/8-13 - * ABC--DE-F - * findPositions(1, 4) returns Range(9, 9) // B only - * findPositions(3, 4) returns null // all gaps - * findPositions(2, 6) returns Range(10, 12) // CDE - * findPositions(3, 7) returns Range(11,12) // DE - *- * - * @param fromCol - * first aligned column position (base 0, inclusive) - * @param toCol - * last aligned column position (base 0, inclusive) + * Returns the from-to sequence positions (start..) for the given column + * positions (1..), or null if no residues are included in the range * + * @param fromColum + * @param toColumn * @return */ - public Range findPositions(int fromCol, int toCol); + public Range findPositions(int fromColum, int toColumn); /** * Returns an int array where indices correspond to each residue in the @@ -235,6 +222,13 @@ public interface SequenceI extends ASequenceI public int[] gapMap(); /** + * Build a bitset corresponding to sequence gaps + * + * @return a BitSet where set values correspond to gaps in the sequence + */ + public BitSet gapBitset(); + + /** * Returns an int array where indices correspond to each position in sequence * char array and the element value gives the result of findPosition for that * index in the sequence. @@ -289,7 +283,7 @@ public interface SequenceI extends ASequenceI * Answers a list of all sequence features associated with this sequence. The * list may be held by the sequence's dataset sequence if that is defined. * - * @return hard reference to array + * @return */ public List