X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=48615f0dea44b380d39724b8292df2bef2384c79;hb=cfa118f7383e300235afb04ec0e093bf4e50b928;hp=b22e48f8613a26b394ed688078c196cfff88f826;hpb=acf6d0deb9caf0148791f2993be0a2cd7987f569;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index b22e48f..48615f0 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -21,6 +21,7 @@ package jalview.datamodel; import jalview.datamodel.features.SequenceFeaturesI; +import jalview.util.MapList; import java.util.BitSet; import java.util.Iterator; @@ -205,11 +206,14 @@ public interface SequenceI extends ASequenceI public int findPosition(int i); /** - * Returns the from-to sequence positions (start..) for the given column - * positions (1..), or null if no residues are included in the range + * Returns the sequence positions for first and last residues lying within the + * given column positions [fromColum,toColumn] (where columns are numbered + * from 1), or null if no residues are included in the range * * @param fromColum + * - first column base 1 * @param toColumn + * - last column, base 1 * @return */ public Range findPositions(int fromColum, int toColumn); @@ -534,6 +538,25 @@ public interface SequenceI extends ASequenceI public int replace(char c1, char c2); /** + * Answers the GeneLociI, or null if not known + * + * @return + */ + GeneLociI getGeneLoci(); + + /** + * Sets the mapping to gene loci for the sequence + * + * @param speciesId + * @param assemblyId + * @param chromosomeId + * @param map + */ + void setGeneLoci(String speciesId, String assemblyId, + String chromosomeId, MapList map); + + + /** * Returns the sequence string constructed from the substrings of a sequence * defined by the int[] ranges provided by an iterator. E.g. the iterator * could iterate over all visible regions of the alignment