X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=3ca759dfdf50c5744d9cfe7fa565a736c6acb5f0;hb=61f1a8b75ea5ce352d6214c34fbdcd58bafbbb73;hp=e9259ddab23903e495451276e718476a4c2617eb;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index e9259dd..3ca759d 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -20,6 +20,7 @@ */ package jalview.datamodel; +import java.util.List; import java.util.Vector; import fr.orsay.lri.varna.models.rna.RNA; @@ -136,10 +137,12 @@ public interface SequenceI * create a new sequence object from start to end of this sequence * * @param start - * int + * int index for start position * @param end - * int + * int index for end position + * * @return SequenceI + * @note implementations may use getSequence to get the sequence data */ public SequenceI getSubSequence(int start, int end); @@ -188,7 +191,7 @@ public interface SequenceI * Returns the sequence position for an alignment position * * @param i - * column index in alignment (from 1) + * column index in alignment (from 0.. getAlignmentAnnotations(String calcId, + String label); + + /** * create a new dataset sequence (if necessary) for this sequence and sets * this sequence to refer to it. This call will move any features or - * references on the sequence onto the dataset. + * references on the sequence onto the dataset. It will also make a duplicate + * of existing annotation rows for the dataset sequence, rather than relocate + * them in order to preserve external references (since 2.8.2). * * @return dataset sequence for this sequence */ @@ -352,7 +369,9 @@ public interface SequenceI /** * Transfer any database references or annotation from entry under a sequence - * mapping. + * mapping.
+ * Note: DOES NOT transfer sequence associated alignment + * annotation
* * @param entry * @param mp