/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
+import jalview.api.DBRefEntryI;
+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 String getSequenceAsString();
/**
- * get a range on the seuqence as a string
+ * get a range on the sequence as a string
*
* @param start
- * DOCUMENT ME!
+ * position relative to start of sequence including gaps (from 0)
* @param end
- * DOCUMENT ME!
+ * position relative to start of sequence including gaps (from 0)
*
- * @return DOCUMENT ME!
+ * @return String containing all gap and symbols in specified range
*/
public String getSequenceAsString(int start, int end);
/**
- * DOCUMENT ME!
+ * Get the sequence as a character array
*
- * @return DOCUMENT ME!
+ * @return seqeunce and any gaps
*/
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);
/**
* Return the alignment column for a sequence position
- * * Return the alignment position for a sequence position
*
* @param pos
* lying from start to end
*
- * @return aligned column for residue (0 if residue is upstream from alignment, -1 if residue is downstream from alignment)
- * note. Sequence object returns sequence.getEnd() for positions upstream currently. TODO: change sequence for assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
+ * @return aligned column for residue (0 if residue is upstream from
+ * alignment, -1 if residue is downstream from alignment) note.
+ * Sequence object returns sequence.getEnd() for positions upstream
+ * currently. TODO: change sequence for
+ * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
*
*/
public int findIndex(int pos);
* 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();
/**
+ *
+ * @return true if sequence is composed of amino acid characters
+ */
+ 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
+ * @param position
* DOCUMENT ME!
- * @param c
+ * @param ch
* DOCUMENT ME!
*/
- 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
public void setVamsasId(String id);
- public void setDBRef(DBRefEntry[] dbs);
+ 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 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);
+
+ /**
* 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
* null or mapping from entry's numbering to local start/end
*/
public void transferAnnotation(SequenceI entry, Mapping mp);
-
+
/**
- * @param index The sequence index in the MSA
+ * @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
*/
-
+
public RNA getRNA();
-
+
/**
- * @param rna The RNA.
+ * @param rna
+ * The RNA.
*/
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);
+
+ /**
+ * Set the distinct source database, and accession number from which a
+ * sequence and its start-end data were derived from. This is very important
+ * for SIFTS mappings and must be set prior to performing SIFTS mapping.
+ *
+ * @param dbRef
+ * the source dbRef for the sequence
+ */
+ public void setSourceDBRef(DBRefEntryI dbRef);
+
+ /**
+ * Get the distinct source database, and accession number from which a
+ * sequence and its start-end data were derived from.
+ *
+ * @return
+ */
+ public DBRefEntryI getSourceDBRef();
}
git://source.jalview.org / jalview.git / blobdiff