2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.datamodel;
23 import jalview.datamodel.features.SequenceFeaturesI;
25 import java.util.BitSet;
26 import java.util.List;
27 import java.util.Vector;
29 import fr.orsay.lri.varna.models.rna.RNA;
32 * Methods for manipulating a sequence, its metadata and related annotation in
33 * an alignment or dataset.
38 public interface SequenceI extends ASequenceI
41 * Set the display name for the sequence
45 public void setName(String name);
48 * Get the display name
50 public String getName();
53 * Set start position of first non-gapped symbol in sequence
58 public void setStart(int start);
61 * get start position of first non-gapped residue in sequence
65 public int getStart();
68 * get the displayed id of the sequence
70 * @return true means the id will be returned in the form
71 * DisplayName/Start-End
73 public String getDisplayId(boolean jvsuffix);
76 * set end position for last residue in sequence
80 public void setEnd(int end);
83 * get end position for last residue in sequence getEnd()>getStart() unless
84 * sequence only consists of gap characters
91 * @return length of sequence including gaps
94 public int getLength();
97 * Replace the sequence with the given string
100 * new sequence string
102 public void setSequence(String sequence);
105 * @return sequence as string
107 public String getSequenceAsString();
110 * get a range on the sequence as a string
113 * position relative to start of sequence including gaps (from 0)
115 * position relative to start of sequence including gaps (from 0)
117 * @return String containing all gap and symbols in specified range
119 public String getSequenceAsString(int start, int end);
122 * Answers a copy of the sequence as a character array
126 public char[] getSequence();
129 * get stretch of sequence characters in an array
132 * absolute index into getSequence()
134 * exclusive index of last position in segment to be returned.
136 * @return char[max(0,end-start)];
138 public char[] getSequence(int start, int end);
141 * create a new sequence object with a subsequence of this one but sharing the
142 * same dataset sequence
145 * int index for start position (base 0, inclusive)
147 * int index for end position (base 0, exclusive)
150 * @note implementations may use getSequence to get the sequence data
152 public SequenceI getSubSequence(int start, int end);
155 * get the i'th character in this sequence's local reference frame (ie from
156 * 0-number of characters lying from start-end)
160 * @return character or ' '
162 public char getCharAt(int i);
170 public void setDescription(String desc);
175 * @return DOCUMENT ME!
177 public String getDescription();
180 * Return the alignment column (from 1..) for a sequence position
183 * lying from start to end
185 * @return aligned column for residue (0 if residue is upstream from
186 * alignment, -1 if residue is downstream from alignment) note.
187 * Sequence object returns sequence.getEnd() for positions upstream
188 * currently. TODO: change sequence for
189 * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
192 public int findIndex(int pos);
195 * Returns the sequence position for an alignment position.
198 * column index in alignment (from 0..<length)
200 * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
203 public int findPosition(int i);
206 * Returns the sequence positions for first and last residues lying within the
207 * given column positions [fromColum,toColumn] (where columns are numbered
208 * from 1), or null if no residues are included in the range
211 * - first column base 1
213 * - last column, base 1
216 public Range findPositions(int fromColum, int toColumn);
219 * Returns an int array where indices correspond to each residue in the
220 * sequence and the element value gives its position in the alignment
222 * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
223 * residues in SequenceI object
225 public int[] gapMap();
228 * Returns an int array where indices correspond to each position in sequence
229 * char array and the element value gives the result of findPosition for that
230 * index in the sequence.
232 * @return int[SequenceI.getLength()]
234 public int[] findPositionMap();
237 * Answers true if the sequence is composed of amino acid characters. Note
238 * that implementations may use heuristic methods which are not guaranteed to
239 * give the biologically 'right' answer.
243 public boolean isProtein();
246 * Delete a range of aligned sequence columns, creating a new dataset sequence
247 * if necessary and adjusting start and end positions accordingly.
250 * first column in range to delete (inclusive)
252 * last column in range to delete (exclusive)
254 public void deleteChars(int i, int j);
260 * alignment column number
262 * character to insert
264 public void insertCharAt(int i, char c);
267 * insert given character at alignment column position
270 * alignment column number
274 * character to insert
276 public void insertCharAt(int position, int count, char ch);
279 * Answers a list of all sequence features associated with this sequence. The
280 * list may be held by the sequence's dataset sequence if that is defined.
284 public List<SequenceFeature> getSequenceFeatures();
287 * Answers the object holding features for the sequence
291 SequenceFeaturesI getFeatures();
294 * Replaces the sequence features associated with this sequence with the given
295 * features. If this sequence has a dataset sequence, then this method will
296 * update the dataset sequence's features instead.
300 public void setSequenceFeatures(List<SequenceFeature> features);
308 public void setPDBId(Vector<PDBEntry> ids);
313 * @return DOCUMENT ME!
315 public Vector<PDBEntry> getAllPDBEntries();
318 * Adds the entry to the *normalised* list of PDBIds.
320 * If a PDBEntry is passed with the same entry.getID() string as one already
321 * in the list, or one is added that appears to be the same but has a chain ID
322 * appended, then the existing PDBEntry will be updated with the new
323 * attributes instead, unless the entries have distinct chain codes or
324 * associated structure files.
327 * @return true if the entry was added, false if updated
329 public boolean addPDBId(PDBEntry entry);
332 * update the list of PDBEntrys to include any DBRefEntrys citing structural
335 * @return true if PDBEntry list was modified
337 public boolean updatePDBIds();
339 public String getVamsasId();
341 public void setVamsasId(String id);
344 * set the array of Database references for the sequence.
347 * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
348 * set are not normalised.
351 public void setDBRefs(DBRefEntry[] dbs);
353 public DBRefEntry[] getDBRefs();
356 * add the given entry to the list of DBRefs for this sequence, or replace a
357 * similar one if entry contains a map object and the existing one doesnt.
361 public void addDBRef(DBRefEntry entry);
364 * Adds the given sequence feature and returns true, or returns false if it is
365 * already present on the sequence, or if the feature type is null.
370 public boolean addSequenceFeature(SequenceFeature sf);
372 public void deleteFeature(SequenceFeature sf);
374 public void setDatasetSequence(SequenceI seq);
376 public SequenceI getDatasetSequence();
379 * Returns a new array containing this sequence's annotations, or null.
381 public AlignmentAnnotation[] getAnnotation();
384 * Returns true if this sequence has the given annotation (by object
387 public boolean hasAnnotation(AlignmentAnnotation ann);
390 * Add the given annotation, if not already added, and set its sequence ref to
391 * be this sequence. Does nothing if this sequence's annotations already
392 * include this annotation (by identical object reference).
394 public void addAlignmentAnnotation(AlignmentAnnotation annotation);
396 public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
399 * Derive a sequence (using this one's dataset or as the dataset)
401 * @return duplicate sequence with valid dataset sequence
403 public SequenceI deriveSequence();
406 * set the array of associated AlignmentAnnotation for this sequenceI
410 public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
413 * Get one or more alignment annotations with a particular label.
416 * string which each returned annotation must have as a label.
417 * @return null or array of annotations.
419 public AlignmentAnnotation[] getAnnotation(String label);
422 * Returns a (possibly empty) list of any annotations that match on given
423 * calcId (source) and label (type). Null values do not match.
428 public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
432 * create a new dataset sequence (if necessary) for this sequence and sets
433 * this sequence to refer to it. This call will move any features or
434 * references on the sequence onto the dataset. It will also make a duplicate
435 * of existing annotation rows for the dataset sequence, rather than relocate
436 * them in order to preserve external references (since 2.8.2).
438 * @return dataset sequence for this sequence
440 public SequenceI createDatasetSequence();
443 * Transfer any database references or annotation from entry under a sequence
445 * <strong>Note: DOES NOT transfer sequence associated alignment annotation
450 * null or mapping from entry's numbering to local start/end
452 public void transferAnnotation(SequenceI entry, Mapping mp);
456 * The sequence index in the MSA
458 public void setIndex(int index);
461 * @return The index of the sequence in the alignment
463 public int getIndex();
466 * @return The RNA of the sequence in the alignment
475 public void setRNA(RNA rna);
479 * @return list of insertions (gap characters) in sequence
481 public List<int[]> getInsertions();
484 * Given a pdbId String, return the equivalent PDBEntry if available in the
490 public PDBEntry getPDBEntry(String pdbId);
493 * Get all primary database/accessions for this sequence's data. These
494 * DBRefEntry are expected to resolve to a valid record in the associated
495 * external database, either directly or via a provided 1:1 Mapping.
497 * @return just the primary references (if any) for this sequence, or an empty
500 public List<DBRefEntry> getPrimaryDBRefs();
503 * Returns a (possibly empty) list of sequence features that overlap the given
504 * alignment column range, optionally restricted to one or more specified
505 * feature types. If the range is all gaps, then features which enclose it are
506 * included (but not contact features).
509 * start column of range inclusive (1..)
511 * end column of range inclusive (1..)
513 * optional feature types to restrict results to
516 List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
519 * Method to call to indicate that the sequence (characters or alignment/gaps)
520 * has been modified. Provided to allow any cursors on residue/column
521 * positions to be invalidated.
523 void sequenceChanged();
527 * @return BitSet corresponding to index [0,length) where Comparison.isGap()
530 BitSet getInsertionsAsBits();
533 * Replaces every occurrence of c1 in the sequence with c2 and returns the
534 * number of characters changed
539 int replace(char c1, char c2);