X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=163a4a043fe239144a5092a9e1329aefa35fac74;hb=480d7b96f089281a3caf77d2a4e5adec09dc5bfa;hp=75394b18c873ceb26e87fefecaf6ac5cb025e95f;hpb=51728d3951398f9c12d7017c776953f17322cc68;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 75394b1..163a4a0 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -20,6 +20,8 @@ */ package jalview.datamodel; +import jalview.datamodel.features.SequenceFeaturesI; + import java.util.List; import java.util.Vector; @@ -174,7 +176,7 @@ public interface SequenceI extends ASequenceI public String getDescription(); /** - * Return the alignment column for a sequence position + * Return the alignment column (from 1..) for a sequence position * * @param pos * lying from start to end @@ -199,6 +201,30 @@ 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) + * + * @return + */ + public Range findPositions(int fromCol, int toCol); + + /** * Returns an int array where indices correspond to each residue in the * sequence and the element value gives its position in the alignment * @@ -259,22 +285,28 @@ public interface SequenceI extends ASequenceI public void insertCharAt(int position, int count, char ch); /** - * Gets array holding sequence features associated with this sequence. The - * array may be held by the sequence's dataset sequence if that is defined. + * 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 */ - public SequenceFeature[] getSequenceFeatures(); + public List