/*
- * 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.
*
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 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 for a sequence position
*
* @param pos
* lying from start to end
* Returns the sequence position for an alignment 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
*/
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!
+ * Gets array holding sequence features associated with this sequence. The
+ * array may be held by the sequence's dataset sequence if that is defined.
*
- * @return DOCUMENT ME!
+ * @return hard reference to array
*/
public SequenceFeature[] getSequenceFeatures();
/**
- * DOCUMENT ME!
+ * 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
*
- * @param v
- * DOCUMENT ME!
+ * @param features
+ * New array of sequence features
*/
public void setSequenceFeatures(SequenceFeature[] features);
* @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.
+ *
+ * @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[] getDBRef();
+ public 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
+ *
+ * @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);
/**
- * Return a list of any annotations which match the given calcId (source) and
- * label (type). Null values do not match.
+ * 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
- * @return
*/
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label);
/**
* Transfer any database references or annotation from entry under a sequence
* mapping. <br/>
- * <strong>Note: DOES NOT transfer sequence associated alignment
- * annotation </strong><br/>
+ * <strong>Note: DOES NOT transfer sequence associated alignment annotation
+ * </strong><br/>
*
* @param entry
* @param mp
*/
public void setRNA(RNA rna);
+ /**
+ *
+ * @return list of insertions (gap characters) in sequence
+ */
+ public List<int[]> 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<DBRefEntry> getPrimaryDBRefs();
}