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 java.util.List;
24 import java.util.Vector;
26 import fr.orsay.lri.varna.models.rna.RNA;
34 public interface SequenceI
37 * Set the display name for the sequence
41 public void setName(String name);
44 * Get the display name
46 public String getName();
49 * Set start position of first non-gapped symbol in sequence
54 public void setStart(int start);
57 * get start position of first non-gapped residue in sequence
61 public int getStart();
64 * get the displayed id of the sequence
66 * @return true means the id will be returned in the form
67 * DisplayName/Start-End
69 public String getDisplayId(boolean jvsuffix);
72 * set end position for last residue in sequence
76 public void setEnd(int end);
79 * get end position for last residue in sequence getEnd()>getStart() unless
80 * sequence only consists of gap characters
87 * @return length of sequence including gaps
90 public int getLength();
93 * Replace the sequence with the given string
98 public void setSequence(String sequence);
101 * @return sequence as string
103 public String getSequenceAsString();
106 * get a range on the sequence as a string
109 * position relative to start of sequence including gaps (from 0)
111 * position relative to start of sequence including gaps (from 0)
113 * @return String containing all gap and symbols in specified range
115 public String getSequenceAsString(int start, int end);
118 * Get the sequence as a character array
120 * @return seqeunce and any gaps
122 public char[] getSequence();
125 * get stretch of sequence characters in an array
128 * absolute index into getSequence()
130 * exclusive index of last position in segment to be returned.
132 * @return char[max(0,end-start)];
134 public char[] getSequence(int start, int end);
137 * create a new sequence object with a subsequence of this one but sharing the
138 * same dataset sequence
141 * int index for start position (base 0, inclusive)
143 * int index for end position (base 0, exclusive)
146 * @note implementations may use getSequence to get the sequence data
148 public SequenceI getSubSequence(int start, int end);
151 * get the i'th character in this sequence's local reference frame (ie from
152 * 0-number of characters lying from start-end)
156 * @return character or ' '
158 public char getCharAt(int i);
166 public void setDescription(String desc);
171 * @return DOCUMENT ME!
173 public String getDescription();
176 * Return the alignment column for a sequence position
179 * lying from start to end
181 * @return aligned column for residue (0 if residue is upstream from
182 * alignment, -1 if residue is downstream from alignment) note.
183 * Sequence object returns sequence.getEnd() for positions upstream
184 * currently. TODO: change sequence for
185 * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
188 public int findIndex(int pos);
191 * Returns the sequence position for an alignment position
194 * column index in alignment (from 0..<length)
196 * @return residue number for residue (left of and) nearest ith column
198 public int findPosition(int i);
201 * Returns an int array where indices correspond to each residue in the
202 * sequence and the element value gives its position in the alignment
204 * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
205 * residues in SequenceI object
207 public int[] gapMap();
210 * Returns an int array where indices correspond to each position in sequence
211 * char array and the element value gives the result of findPosition for that
212 * index in the sequence.
214 * @return int[SequenceI.getLength()]
216 public int[] findPositionMap();
219 * Delete a range of aligned sequence columns, creating a new dataset sequence
220 * if necessary and adjusting start and end positions accordingly.
223 * first column in range to delete (inclusive)
225 * last column in range to delete (exclusive)
227 public void deleteChars(int i, int j);
237 public void insertCharAt(int i, char c);
246 public void insertCharAt(int position, int count, char ch);
251 * @return DOCUMENT ME!
253 public SequenceFeature[] getSequenceFeatures();
261 public void setSequenceFeatures(SequenceFeature[] features);
269 public void setPDBId(Vector<PDBEntry> ids);
274 * @return DOCUMENT ME!
276 public Vector<PDBEntry> getPDBId();
279 * add entry to the vector of PDBIds, if it isn't in the list already
283 public void addPDBId(PDBEntry entry);
286 * update the list of PDBEntrys to include any DBRefEntrys citing structural
289 * @return true if PDBEntry list was modified
291 public boolean updatePDBIds();
293 public String getVamsasId();
295 public void setVamsasId(String id);
297 public void setDBRef(DBRefEntry[] dbs);
299 public DBRefEntry[] getDBRef();
302 * add the given entry to the list of DBRefs for this sequence, or replace a
303 * similar one if entry contains a map object and the existing one doesnt.
307 public void addDBRef(DBRefEntry entry);
309 public void addSequenceFeature(SequenceFeature sf);
311 public void deleteFeature(SequenceFeature sf);
313 public void setDatasetSequence(SequenceI seq);
315 public SequenceI getDatasetSequence();
318 * Returns a new array containing this sequence's annotations, or null.
320 public AlignmentAnnotation[] getAnnotation();
323 * Returns true if this sequence has the given annotation (by object
326 public boolean hasAnnotation(AlignmentAnnotation ann);
329 * Add the given annotation, if not already added, and set its sequence ref to
330 * be this sequence. Does nothing if this sequence's annotations already
331 * include this annotation (by identical object reference).
333 public void addAlignmentAnnotation(AlignmentAnnotation annotation);
335 public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
338 * Derive a sequence (using this one's dataset or as the dataset)
340 * @return duplicate sequence with valid dataset sequence
342 public SequenceI deriveSequence();
345 * set the array of associated AlignmentAnnotation for this sequenceI
349 public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
352 * Get one or more alignment annotations with a particular label.
355 * string which each returned annotation must have as a label.
356 * @return null or array of annotations.
358 public AlignmentAnnotation[] getAnnotation(String label);
361 * Returns a (possibly empty) list of any annotations that match on given
362 * calcId (source) and label (type). Null values do not match.
367 public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
371 * create a new dataset sequence (if necessary) for this sequence and sets
372 * this sequence to refer to it. This call will move any features or
373 * references on the sequence onto the dataset. It will also make a duplicate
374 * of existing annotation rows for the dataset sequence, rather than relocate
375 * them in order to preserve external references (since 2.8.2).
377 * @return dataset sequence for this sequence
379 public SequenceI createDatasetSequence();
382 * Transfer any database references or annotation from entry under a sequence
384 * <strong>Note: DOES NOT transfer sequence associated alignment
385 * annotation </strong><br/>
389 * null or mapping from entry's numbering to local start/end
391 public void transferAnnotation(SequenceI entry, Mapping mp);
395 * The sequence index in the MSA
397 public void setIndex(int index);
400 * @return The index of the sequence in the alignment
402 public int getIndex();
405 * @return The RNA of the sequence in the alignment
414 public void setRNA(RNA rna);
418 * @return list of insertions (gap characters) in sequence
420 public List<int[]> getInsertions();