X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=7c3eb41fa8f4a598d9a8ea4daf2e333d1c2f2bf6;hb=ca47e4d0e1176893b414fba3fbe8a308e24cc52e;hp=78311e49af115ad83c86f7d6f70c245ac20aa7dd;hpb=a81fc6261c0b196fe62f37bcbec72446109bb452;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 78311e4..7c3eb41 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,18 +20,26 @@ */ 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; import fr.orsay.lri.varna.models.rna.RNA; /** - * DOCUMENT ME! + * Methods for manipulating a sequence, its metadata and related annotation in + * an alignment or dataset. * * @author $author$ * @version $Revision$ */ -public interface SequenceI +public interface SequenceI extends ASequenceI { /** * Set the display name for the sequence @@ -106,18 +114,20 @@ public interface SequenceI * 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(); @@ -134,12 +144,13 @@ public interface SequenceI public char[] getSequence(int start, int end); /** - * create a new sequence object from start to end of this sequence + * create a new sequence object with a subsequence of this one but sharing the + * same dataset sequence * * @param start - * int index for start position + * int index for start position (base 0, inclusive) * @param end - * int index for end position + * int index for end position (base 0, exclusive) * * @return SequenceI * @note implementations may use getSequence to get the sequence data @@ -172,8 +183,7 @@ public interface SequenceI public String getDescription(); /** - * Return the alignment column for a sequence position * Return the alignment - * position for a sequence position + * Return the alignment column (from 1..) for a sequence position * * @param pos * lying from start to end @@ -188,16 +198,31 @@ public interface SequenceI 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(); /** - * DOCUMENT ME! + * Answers the object holding features for the sequence * - * @param v - * DOCUMENT ME! + * @return */ - public void setSequenceFeatures(SequenceFeature[] features); + 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 + */ + public void setSequenceFeatures(List features); /** * DOCUMENT ME! @@ -267,21 +319,28 @@ public interface SequenceI * @param id * DOCUMENT ME! */ - public void setPDBId(Vector ids); + public void setPDBId(Vector ids); /** - * DOCUMENT ME! + * Returns a list * * @return DOCUMENT ME! */ - public Vector getPDBId(); + 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 @@ -295,9 +354,20 @@ public interface SequenceI public void setVamsasId(String id); - public void setDBRef(DBRefEntry[] dbs); + /** + * 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(DBModList dbs); - public DBRefEntry[] getDBRef(); + public DBModList getDBRefs(); /** * add the given entry to the list of DBRefs for this sequence, or replace a @@ -307,7 +377,14 @@ public interface SequenceI */ 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); @@ -369,6 +446,17 @@ public interface SequenceI 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 @@ -382,8 +470,8 @@ public interface SequenceI /** * Transfer any database references or annotation from entry under a sequence * mapping.
- * Note: DOES NOT transfer sequence associated alignment - * annotation
+ * Note: DOES NOT transfer sequence associated alignment annotation + *
* * @param entry * @param mp @@ -392,17 +480,6 @@ public interface SequenceI 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 */ @@ -420,4 +497,104 @@ public interface SequenceI */ public List getInsertions(); + /** + * Given a pdbId String, return the equivalent PDBEntry if available in the + * given sequence + * + * @param pdbId + * @return + */ + public PDBEntry getPDBEntry(String pdbId); + + /** + * 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(); + + /** + * 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); + + /** + * 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); + + } +