/*
- * 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.
*
*/
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
*/
public void setName(String name);
+ public HiddenMarkovModel getHMM();
+
+ public void setHMM(HiddenMarkovModel hmm);
/**
* Get the display name
*/
* 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();
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
+ * int index for start position (base 0, inclusive)
* @param end
- * int
+ * int index for end position (base 0, exclusive)
+ *
* @return SequenceI
+ * @note implementations may use getSequence to get the sequence data
*/
public SequenceI getSubSequence(int start, int end);
/**
- * DOCUMENT ME!
+ * get the i'th character in this sequence's local reference frame (ie from
+ * 0-number of characters lying from start-end)
*
* @param i
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * index
+ * @return character or ' '
*/
public char getCharAt(int i);
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
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 1)
+ * column index in alignment (from 0..<length)
*
- * @return residue number for residue (left of and) nearest ith column
+ * @return
*/
public int findPosition(int i);
/**
+ * 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. (0 and negative positions are rounded up)
+ * @param toColumn
+ * - last column, base 1
+ * @return null if fromColum>toColumn
+ */
+ public ContiguousI findPositions(int fromColum, int toColumn);
+
+ /**
* Returns an int array where indices correspond to each residue in the
* sequence and the element value gives its position in the alignment
*
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.
public int[] findPositionMap();
/**
+ * Answers true if the sequence is composed of amino acid characters. Note
+ * that implementations may use heuristic methods which are not guaranteed to
+ * give the biologically 'right' answer.
+ *
+ * @return
+ */
+ public boolean isProtein();
+
+ /**
* Delete a range of aligned sequence columns, creating a new dataset sequence
* if necessary and adjusting start and end positions accordingly.
*
* @param i
- * first column in range to delete
+ * first column in range to delete (inclusive)
* @param j
- * last column in range to delete
+ * last column in range to delete (exclusive)
*/
public void deleteChars(int i, int j);
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * alignment column number
* @param c
- * DOCUMENT ME!
+ * character to insert
*/
public void insertCharAt(int i, char c);
/**
- * DOCUMENT ME!
+ * insert given character at alignment column position
*
- * @param i
- * DOCUMENT ME!
- * @param c
- * DOCUMENT ME!
+ * @param position
+ * alignment column number
+ * @param count
+ * length of insert
+ * @param ch
+ * character to insert
*/
- public void insertCharAt(int i, int length, char c);
+ public void insertCharAt(int position, int count, char ch);
/**
- * DOCUMENT ME!
+ * Answers a list of all sequence features associated with this sequence. The
+ * list may be held by the sequence's dataset sequence if that is defined.
*
- * @return DOCUMENT ME!
+ * @return
*/
- public SequenceFeature[] getSequenceFeatures();
+ public List<SequenceFeature> getSequenceFeatures();
/**
- * DOCUMENT ME!
+ * Answers the object holding features for the sequence
*
- * @param v
- * DOCUMENT ME!
+ * @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
*/
- public void setSequenceFeatures(SequenceFeature[] features);
+ public void setSequenceFeatures(List<SequenceFeature> features);
/**
* DOCUMENT ME!
* @param id
* DOCUMENT ME!
*/
- public void setPDBId(Vector ids);
+ public void setPDBId(Vector<PDBEntry> ids);
/**
- * DOCUMENT ME!
+ * Returns a list
*
* @return DOCUMENT ME!
*/
- public Vector getPDBId();
+ public Vector<PDBEntry> 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
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<DBRefEntry> dbs);
- public DBRefEntry[] getDBRef();
+ public DBModList<DBRefEntry> getDBRefs();
/**
* add the given entry to the list of DBRefs for this sequence, or replace a
*/
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);
public SequenceI getDatasetSequence();
+ /**
+ * Returns a new array containing this sequence's annotations, or null.
+ */
public AlignmentAnnotation[] getAnnotation();
+ /**
+ * Returns true if this sequence has the given annotation (by object
+ * identity).
+ */
+ public boolean hasAnnotation(AlignmentAnnotation ann);
+
+ /**
+ * Add the given annotation, if not already added, and set its sequence ref to
+ * be this sequence. Does nothing if this sequence's annotations already
+ * include this annotation (by identical object reference).
+ */
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
public AlignmentAnnotation[] getAnnotation(String label);
/**
+ * Returns a (possibly empty) list of any annotations that match on given
+ * calcId (source) and label (type). Null values do not match.
+ *
+ * @param calcId
+ * @param label
+ */
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ 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<AlignmentAnnotation> 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.
+ * references on the sequence onto the dataset. It will also make a duplicate
+ * of existing annotation rows for the dataset sequence, rather than relocate
+ * them in order to preserve external references (since 2.8.2).
*
* @return dataset sequence for this sequence
*/
/**
* Transfer any database references or annotation from entry under a sequence
- * mapping.
+ * mapping. <br/>
+ * <strong>Note: DOES NOT transfer sequence associated alignment annotation
+ * </strong><br/>
*
* @param entry
* @param mp
public void transferAnnotation(SequenceI entry, Mapping mp);
/**
- * @param index
- * The sequence index in the MSA
+ * @return The RNA of the sequence in the alignment
*/
- public void setIndex(int index);
+
+ public RNA getRNA();
/**
- * @return The index of the sequence in the alignment
+ * @param rna
+ * The RNA.
*/
- public int getIndex();
-
+ public void setRNA(RNA rna);
+
/**
- * @return The RNA of the sequence in the alignment
+ *
+ * @return list of insertions (gap characters) in sequence
*/
-
- public RNA getRNA();
-
+ public List<int[]> getInsertions();
+
/**
- * @param rna The RNA.
+ * Given a pdbId String, return the equivalent PDBEntry if available in the
+ * given sequence
+ *
+ * @param pdbId
+ * @return
*/
- public void setRNA(RNA rna);
+ 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<DBRefEntry> 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<SequenceFeature> 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<int[]> 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<int[]> it);
+
+
+ /**
+ * Answers true if this sequence has an associated Hidden Markov Model
+ *
+ * @return
+ */
+ boolean hasHMMProfile();
}
+