X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=2e1daa3976970a15875c47eba74402aba7192e9b;hb=19c22459dca6c69d6f1fd0eed029c01e21c99854;hp=e4be5ee3dd299f7f7e46844082f8e2f580e3f318;hpb=df2bf54c7050c42db156e96e73bbabce63e718d7;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index e4be5ee..2e1daa3 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -20,12 +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 @@ -34,7 +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 @@ -109,18 +113,20 @@ 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 */ public String getSequenceAsString(int start, int end); /** - * Get the sequence as a character array + * Answers a copy of the sequence as a character array * - * @return seqeunce and any gaps + * @return */ public char[] getSequence(); @@ -176,7 +182,7 @@ public interface SequenceI extends ASequenceI public String getDescription(); /** - * Return the alignment column for a sequence position + * Return the alignment column (from 1..) for a sequence position * * @param pos * lying from start to end @@ -191,16 +197,31 @@ 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.. getSequenceFeatures(); @@ -328,14 +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 @@ -383,7 +415,7 @@ 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(); @@ -414,6 +446,18 @@ 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 @@ -437,17 +481,6 @@ public interface SequenceI extends ASequenceI public void transferAnnotation(SequenceI entry, Mapping mp); /** - * @param index - * The sequence index in the MSA - */ - public void setIndex(int index); - - /** - * @return The index of the sequence in the alignment - */ - public int getIndex(); - - /** * @return The RNA of the sequence in the alignment */ @@ -485,14 +518,85 @@ public interface SequenceI extends ASequenceI public List getPrimaryDBRefs(); /** - * Returns a (possibly empty) list of sequence features that overlap the range - * from-to (inclusive), optionally restricted to one or more specified feature - * types + * Returns a (possibly empty) list of sequence features that overlap the given + * alignment column range, optionally restricted to one or more specified + * feature types. If the range is all gaps, then features which enclose it are + * included (but not contact features). * - * @param from - * @param to + * @param fromCol + * start column of range inclusive (1..) + * @param toCol + * end column of range inclusive (1..) * @param types + * optional feature types to restrict results to * @return */ - List findFeatures(int from, int to, String... types); + List findFeatures(int fromCol, int toCol, + String... types); + + /** + * Method to call to indicate that the sequence (characters or alignment/gaps) + * has been modified. Provided to allow any cursors on residue/column + * positions to be invalidated. + */ + void sequenceChanged(); + + /** + * + * @return BitSet corresponding to index [0,length) where Comparison.isGap() + * returns true. + */ + BitSet getInsertionsAsBits(); + + /** + * Replaces every occurrence of c1 in the sequence with c2 and returns the + * number of characters changed + * + * @param c1 + * @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); + }