X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=d5114e0aa9ab56e183285670118eec7a234f05ab;hb=HEAD;hp=2f3e92580756a8a839ad4e6af97d9194e81d6ddd;hpb=2b4cc5fb6217217761b4a8bd2529e51b4775a57d;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 2f3e925..d5114e0 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -20,13 +20,16 @@ */ package jalview.datamodel; -import jalview.datamodel.features.SequenceFeaturesI; - import java.util.BitSet; +import java.util.Iterator; import java.util.List; import java.util.Vector; import fr.orsay.lri.varna.models.rna.RNA; +import jalview.datamodel.Sequence.DBModList; +import jalview.datamodel.features.SequenceFeaturesI; +import jalview.util.MapList; +import jalview.ws.params.InvalidArgumentException; /** * Methods for manipulating a sequence, its metadata and related annotation in @@ -35,7 +38,7 @@ import fr.orsay.lri.varna.models.rna.RNA; * @author $author$ * @version $Revision$ */ -public interface SequenceI extends ASequenceI +public interface SequenceI extends ASequenceI, ContactMapHolderI { /** * Set the display name for the sequence @@ -110,9 +113,11 @@ 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 */ @@ -204,14 +209,17 @@ 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); + public ContiguousI findPositions(int fromColum, int toColumn); /** * Returns an int array where indices correspond to each residue in the @@ -223,6 +231,13 @@ 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. @@ -341,14 +356,18 @@ 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 @@ -396,7 +415,8 @@ public interface SequenceI extends ASequenceI /** * Derive a sequence (using this one's dataset or as the dataset) * - * @return duplicate sequence with valid dataset sequence + * @return duplicate sequence and any annotation present with valid dataset + * sequence */ public SequenceI deriveSequence(); @@ -427,6 +447,18 @@ 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 @@ -500,7 +532,8 @@ public interface SequenceI extends ASequenceI * optional feature types to restrict results to * @return */ - List findFeatures(int fromCol, int toCol, String... types); + List findFeatures(int fromCol, int toCol, + String... types); /** * Method to call to indicate that the sequence (characters or alignment/gaps) @@ -508,7 +541,7 @@ public interface SequenceI extends ASequenceI * positions to be invalidated. */ void sequenceChanged(); - + /** * * @return BitSet corresponding to index [0,length) where Comparison.isGap() @@ -524,4 +557,47 @@ 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); + + public void addContactListFor(AlignmentAnnotation annotation, + ContactMatrixI cm); + }