X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=8f1d1602114789394801aaefef5d5ab35f8a5722;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=9ad0a6170bb4f68c674eabf7551ea2aa8c646412;hpb=2353023a8b9d78c2da77f1d17b2ffc41bcec55c7;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 9ad0a61..8f1d160 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -20,9 +20,13 @@ */ 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; import java.util.List; import java.util.Vector; @@ -44,6 +48,9 @@ public interface SequenceI extends ASequenceI */ public void setName(String name); + public HiddenMarkovModel getHMM(); + + public void setHMM(HiddenMarkovModel hmm); /** * Get the display name */ @@ -110,9 +117,11 @@ 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 */ @@ -192,25 +201,29 @@ public interface SequenceI extends ASequenceI public int findIndex(int pos); /** - * Returns the sequence position for an alignment position. + * Returns the sequence position for an alignment (column) position. If at a + * gap, returns the position of the next residue to the right. If beyond the + * end of the sequence, returns 1 more than the last residue position. * * @param i * column index in alignment (from 0..toColumn */ - public Range findPositions(int fromColum, int toColumn); + public ContiguousI findPositions(int fromColum, int toColumn); /** * Returns an int array where indices correspond to each residue in the @@ -222,6 +235,13 @@ 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. @@ -340,14 +360,17 @@ 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 @@ -426,6 +449,17 @@ 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 @@ -484,6 +518,11 @@ public interface SequenceI extends ASequenceI * list */ public List getPrimaryDBRefs(); + /** + * Answers true if the sequence has annotation for Hidden Markov Model + * information content, else false + */ + boolean hasHMMAnnotation(); /** * Returns a (possibly empty) list of sequence features that overlap the given @@ -523,4 +562,53 @@ public interface SequenceI extends ASequenceI * @param c2 */ 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 + * + * @param it + * the iterator to use + * @return a String corresponding to the sequence + */ + public String getSequenceStringFromIterator(Iterator it); + + /** + * Locate the first position in this sequence which is not contained in an + * iterator region. If no such position exists, return 0 + * + * @param it + * iterator over regions + * @return first residue not contained in regions + */ + public int firstResidueOutsideIterator(Iterator it); + + + /** + * Answers true if this sequence has an associated Hidden Markov Model + * + * @return + */ + boolean hasHMMProfile(); } +