/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
-
-import java.awt.*;
+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
{
- /**
- * DOCUMENT ME!
- *
- * @param name DOCUMENT ME!
- */
- public void setName(String name);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName();
-
-
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- */
- public void setStart(int start);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStart();
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getDisplayId(boolean jvsuffix);
-
- /**
- * DOCUMENT ME!
- *
- * @param end DOCUMENT ME!
- */
- public void setEnd(int end);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEnd();
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getLength();
-
- /**
- * DOCUMENT ME!
- *
- * @param sequence DOCUMENT ME!
- */
- public void setSequence(String sequence);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getSequence();
-
- /**
- * DOCUMENT ME!
- *
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getSequence(int start, int end);
- /**
- * create a new sequence object from start to end of this sequence
- * @param start int
- * @param end int
- * @return SequenceI
- */
- public SequenceI getSubSequence(int start, int end);
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getCharAt(int i);
-
- /**
- * DOCUMENT ME!
- *
- * @param desc DOCUMENT ME!
- */
- public void setDescription(String desc);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getDescription();
-
- /**
- * DOCUMENT ME!
- *
- * @param pos DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int findIndex(int pos);
-
- /**
- * Returns the sequence position for an alignment position
- *
- * @param i column index in alignment (from 1)
- *
- * @return residue number for residue (left of and) nearest ith column
- */
- public int findPosition(int i);
-
- /**
- * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
- *
- * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
- */
- public int[] gapMap();
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- */
- public void deleteChars(int i, int j);
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void deleteCharAt(int i);
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param c DOCUMENT ME!
- */
- public void insertCharAt(int i, char c);
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param c DOCUMENT ME!
- */
- public void insertCharAt(int i, int length, char c);
-
-
-
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- */
- public void setColor(Color c);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color getColor();
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceFeature[] getSequenceFeatures();
-
- /**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
- */
- public void setSequenceFeatures(SequenceFeature [] features);
-
- /**
- * DOCUMENT ME!
- *
- * @param id DOCUMENT ME!
- */
- public void setPDBId(Vector ids);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getPDBId();
-
- public void addPDBId(PDBEntry entry);
-
- public String getVamsasId();
-
- public void setVamsasId(String id);
-
- public void setDBRef(DBRefEntry[] dbs);
-
- public DBRefEntry [] getDBRef();
-
- public void addDBRef(DBRefEntry entry);
-
- public void addSequenceFeature(SequenceFeature sf);
-
- public void deleteFeature(SequenceFeature sf);
-
- public void setDatasetSequence(SequenceI seq);
-
- public SequenceI getDatasetSequence();
-
- public AlignmentAnnotation [] getAnnotation();
-
- public void addAlignmentAnnotation(AlignmentAnnotation annotation);
-
- public SequenceGroup getHiddenSequences();
-
- public void addHiddenSequence(SequenceI seq);
-
- public void showHiddenSequence(SequenceI seq);
-
+ /**
+ * Set the display name for the sequence
+ *
+ * @param name
+ */
+ public void setName(String name);
+
+ /**
+ * Get the display name
+ */
+ public String getName();
+
+ /**
+ * Set start position of first non-gapped symbol in sequence
+ *
+ * @param start
+ * new start position
+ */
+ public void setStart(int start);
+
+ /**
+ * get start position of first non-gapped residue in sequence
+ *
+ * @return
+ */
+ public int getStart();
+
+ /**
+ * get the displayed id of the sequence
+ *
+ * @return true means the id will be returned in the form
+ * DisplayName/Start-End
+ */
+ public String getDisplayId(boolean jvsuffix);
+
+ /**
+ * set end position for last residue in sequence
+ *
+ * @param end
+ */
+ public void setEnd(int end);
+
+ /**
+ * get end position for last residue in sequence getEnd()>getStart() unless
+ * sequence only consists of gap characters
+ *
+ * @return
+ */
+ public int getEnd();
+
+ /**
+ * @return length of sequence including gaps
+ *
+ */
+ public int getLength();
+
+ /**
+ * Replace the sequence with the given string
+ *
+ * @param sequence
+ * new sequence string
+ */
+ public void setSequence(String sequence);
+
+ /**
+ * @return sequence as string
+ */
+ public String getSequenceAsString();
+
+ /**
+ * get a range on the sequence as a string
+ *
+ * @param start
+ * position relative to start of sequence including gaps (from 0)
+ * @param end
+ * 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
+ *
+ * @return seqeunce and any gaps
+ */
+ public char[] getSequence();
+
+ /**
+ * get stretch of sequence characters in an array
+ *
+ * @param start
+ * absolute index into getSequence()
+ * @param end
+ * exclusive index of last position in segment to be returned.
+ *
+ * @return char[max(0,end-start)];
+ */
+ public char[] getSequence(int start, int end);
+
+ /**
+ * create a new sequence object with a subsequence of this one but sharing the
+ * same dataset sequence
+ *
+ * @param start
+ * int index for start position (base 0, inclusive)
+ * @param end
+ * 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);
+
+ /**
+ * get the i'th character in this sequence's local reference frame (ie from
+ * 0-number of characters lying from start-end)
+ *
+ * @param i
+ * index
+ * @return character or ' '
+ */
+ public char getCharAt(int i);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc
+ * DOCUMENT ME!
+ */
+ public void setDescription(String desc);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription();
+
+ /**
+ * Return the alignment column 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
+ *
+ */
+ public int findIndex(int pos);
+
+ /**
+ * Returns the sequence position for an alignment position
+ *
+ * @param i
+ * column index in alignment (from 0..<length)
+ *
+ * @return residue number for residue (left of and) nearest ith column
+ */
+ public int findPosition(int i);
+
+ /**
+ * Returns an int array where indices correspond to each residue in the
+ * sequence and the element value gives its position in the alignment
+ *
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
+ * residues in SequenceI object
+ */
+ public int[] gapMap();
+
+ /**
+ * 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.
+ *
+ * @return int[SequenceI.getLength()]
+ */
+ public int[] findPositionMap();
+
+ /**
+ * 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 (inclusive)
+ * @param j
+ * last column in range to delete (exclusive)
+ */
+ public void deleteChars(int i, int j);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ * @param c
+ * DOCUMENT ME!
+ */
+ public void insertCharAt(int i, char c);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param position
+ * DOCUMENT ME!
+ * @param ch
+ * DOCUMENT ME!
+ */
+ public void insertCharAt(int position, int count, char ch);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceFeature[] getSequenceFeatures();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v
+ * DOCUMENT ME!
+ */
+ public void setSequenceFeatures(SequenceFeature[] features);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id
+ * DOCUMENT ME!
+ */
+ public void setPDBId(Vector<PDBEntry> ids);
+
+ /**
+ * Returns a list
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector<PDBEntry> getAllPDBEntries();
+
+ /**
+ * add entry to the vector of PDBIds, if it isn't in the list already
+ *
+ * @param entry
+ */
+ public void addPDBId(PDBEntry entry);
+
+ /**
+ * update the list of PDBEntrys to include any DBRefEntrys citing structural
+ * databases
+ *
+ * @return true if PDBEntry list was modified
+ */
+ public boolean updatePDBIds();
+
+ public String getVamsasId();
+
+ public void setVamsasId(String id);
+
+ public void setDBRef(DBRefEntry[] dbs);
+
+ public DBRefEntry[] getDBRef();
+
+ /**
+ * add the given entry to the list of DBRefs for this sequence, or replace a
+ * similar one if entry contains a map object and the existing one doesnt.
+ *
+ * @param entry
+ */
+ public void addDBRef(DBRefEntry entry);
+
+ public void addSequenceFeature(SequenceFeature sf);
+
+ public void deleteFeature(SequenceFeature sf);
+
+ public void setDatasetSequence(SequenceI seq);
+
+ 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);
+
+ /**
+ * Derive a sequence (using this one's dataset or as the dataset)
+ *
+ * @return duplicate sequence with valid dataset sequence
+ */
+ public SequenceI deriveSequence();
+
+ /**
+ * set the array of associated AlignmentAnnotation for this sequenceI
+ *
+ * @param revealed
+ */
+ public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
+
+ /**
+ * Get one or more alignment annotations with a particular label.
+ *
+ * @param label
+ * string which each returned annotation must have as a label.
+ * @return null or array of annotations.
+ */
+ 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. 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
+ */
+ public SequenceI createDatasetSequence();
+
+ /**
+ * Transfer any database references or annotation from entry under a sequence
+ * 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
+ */
+ 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.
+ */
+ 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);
}
git://source.jalview.org / jalview.git / blobdiff