X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=7c3eb41fa8f4a598d9a8ea4daf2e333d1c2f2bf6;hb=0aa7f6fab658c9a203b410d4bead72217da5c9a0;hp=84643d1265783394d54cb803594f0ed71ade764e;hpb=4a25d1aa51aa9f76efba8eb278bdd976216bb88e;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 84643d1..7c3eb41 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -20,8 +20,10 @@ */ package jalview.datamodel; +import jalview.datamodel.Sequence.DBModList; import jalview.datamodel.features.SequenceFeaturesI; import jalview.util.MapList; +import jalview.ws.params.InvalidArgumentException; import java.util.BitSet; import java.util.Iterator; @@ -112,9 +114,11 @@ public interface SequenceI extends ASequenceI * get a range on the sequence as a string * * @param start - * position relative to start of sequence including gaps (from 0) + * (inclusive) position relative to start of sequence including gaps + * (from 0) * @param end - * position relative to start of sequence including gaps (from 0) + * (exclusive) position relative to start of sequence including gaps + * (from 0) * * @return String containing all gap and symbols in specified range */ @@ -353,14 +357,17 @@ public interface SequenceI extends ASequenceI /** * set the array of Database references for the sequence. * + * BH 2019.02.04 changes param to DBModlist + * * @param dbs * @deprecated - use is discouraged since side-effects may occur if DBRefEntry * set are not normalised. + * @throws InvalidArgumentException if the is not one created by Sequence itself */ @Deprecated - public void setDBRefs(DBRefEntry[] dbs); + public void setDBRefs(DBModList dbs); - public DBRefEntry[] getDBRefs(); + public DBModList getDBRefs(); /** * add the given entry to the list of DBRefs for this sequence, or replace a @@ -439,6 +446,17 @@ public interface SequenceI extends ASequenceI String label); /** + * Returns a (possibly empty) list of any annotations that match on given + * calcId (source), label (type) and description (observation instance). + * Null values do not match. + * + * @param calcId + * @param label + * @param description + */ + public List getAlignmentAnnotations(String calcId, + String label, String description); + /** * 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. It will also make a duplicate @@ -576,4 +594,7 @@ public interface SequenceI extends ASequenceI * @return first residue not contained in regions */ public int firstResidueOutsideIterator(Iterator it); + + } +