X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=d06adcbd4f68b5fefbef332c059de6844ffadca5;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=60040d83117783a28d23a1889c4e28260aa913d6;hpb=935cdb9c4581bd387df656bd29f0804ef5f24c5c;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 60040d8..d06adcb 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -20,8 +20,11 @@ */ package jalview.datamodel; -import jalview.api.DBRefEntryI; +import jalview.datamodel.features.SequenceFeaturesI; +import jalview.util.MapList; +import java.util.BitSet; +import java.util.Iterator; import java.util.List; import java.util.Vector; @@ -43,6 +46,10 @@ public interface SequenceI extends ASequenceI */ public void setName(String name); + public HiddenMarkovModel getHMM(); + + public void setHMM(HiddenMarkovModel hmm); + /** * Get the display name */ @@ -109,18 +116,20 @@ 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 +185,7 @@ 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 +200,31 @@ 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(); /** - * Replaces the array of sequence features associated with this sequence with - * a new array reference. If this sequence has a dataset sequence, then this - * method will update the dataset sequence's feature array + * Answers the object holding features for the sequence + * + * @return + */ + SequenceFeaturesI getFeatures(); + + /** + * Replaces the sequence features associated with this sequence with the given + * features. If this sequence has a dataset sequence, then this method will + * update the dataset sequence's features instead. * * @param features - * New array of sequence features */ - public void setSequenceFeatures(SequenceFeature[] features); + public void setSequenceFeatures(List features); /** * DOCUMENT ME! @@ -283,11 +331,18 @@ public interface SequenceI extends ASequenceI public Vector getAllPDBEntries(); /** - * add entry to the vector of PDBIds, if it isn't in the list already + * Adds the entry to the *normalised* list of PDBIds. + * + * If a PDBEntry is passed with the same entry.getID() string as one already + * in the list, or one is added that appears to be the same but has a chain ID + * appended, then the existing PDBEntry will be updated with the new + * attributes instead, unless the entries have distinct chain codes or + * associated structure files. * * @param entry + * @return true if the entry was added, false if updated */ - public void addPDBId(PDBEntry entry); + public boolean addPDBId(PDBEntry entry); /** * update the list of PDBEntrys to include any DBRefEntrys citing structural @@ -301,6 +356,14 @@ public interface SequenceI extends ASequenceI public void setVamsasId(String id); + /** + * set the array of Database references for the sequence. + * + * @param dbs + * @deprecated - use is discouraged since side-effects may occur if DBRefEntry + * set are not normalised. + */ + @Deprecated public void setDBRefs(DBRefEntry[] dbs); public DBRefEntry[] getDBRefs(); @@ -313,7 +376,14 @@ public interface SequenceI extends ASequenceI */ public void addDBRef(DBRefEntry entry); - public void addSequenceFeature(SequenceFeature sf); + /** + * Adds the given sequence feature and returns true, or returns false if it is + * already present on the sequence, or if the feature type is null. + * + * @param sf + * @return + */ + public boolean addSequenceFeature(SequenceFeature sf); public void deleteFeature(SequenceFeature sf); @@ -398,17 +468,6 @@ 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 */ @@ -435,7 +494,105 @@ public interface SequenceI extends ASequenceI */ public PDBEntry getPDBEntry(String pdbId); - public void setSourceDBRef(DBRefEntryI dbRef); + /** + * Get all primary database/accessions for this sequence's data. These + * DBRefEntry are expected to resolve to a valid record in the associated + * external database, either directly or via a provided 1:1 Mapping. + * + * @return just the primary references (if any) for this sequence, or an empty + * 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 + * 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 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 fromCol, int toCol, String... types); - public DBRefEntryI getSourceDBRef(); + /** + * 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 + */ + 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 + */ + 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 + */ + int firstResidueOutsideIterator(Iterator it); + + /** + * Answers true if this sequence has an associated Hidden Markov Model + * + * @return + */ + boolean hasHMMProfile(); }