2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.datamodel;
22 import java.util.Vector;
24 import fr.orsay.lri.varna.models.rna.RNA;
32 public interface SequenceI
35 * Set the display name for the sequence
39 public void setName(String name);
42 * Get the display name
44 public String getName();
47 * Set start position of first non-gapped symbol in sequence
52 public void setStart(int start);
55 * get start position of first non-gapped residue in sequence
59 public int getStart();
62 * get the displayed id of the sequence
64 * @return true means the id will be returned in the form
65 * DisplayName/Start-End
67 public String getDisplayId(boolean jvsuffix);
70 * set end position for last residue in sequence
74 public void setEnd(int end);
77 * get end position for last residue in sequence getEnd()>getStart() unless
78 * sequence only consists of gap characters
85 * @return length of sequence including gaps
88 public int getLength();
91 * Replace the sequence with the given string
96 public void setSequence(String sequence);
99 * @return sequence as string
101 public String getSequenceAsString();
104 * get a range on the sequence as a string
107 * position relative to start of sequence including gaps (from 0)
109 * position relative to start of sequence including gaps (from 0)
111 * @return String containing all gap and symbols in specified range
113 public String getSequenceAsString(int start, int end);
116 * Get the sequence as a character array
118 * @return seqeunce and any gaps
120 public char[] getSequence();
123 * get stretch of sequence characters in an array
126 * absolute index into getSequence()
128 * exclusive index of last position in segment to be returned.
130 * @return char[max(0,end-start)];
132 public char[] getSequence(int start, int end);
135 * create a new sequence object from start to end of this sequence
143 public SequenceI getSubSequence(int start, int end);
151 * @return DOCUMENT ME!
153 public char getCharAt(int i);
161 public void setDescription(String desc);
166 * @return DOCUMENT ME!
168 public String getDescription();
171 * Return the alignment column for a sequence position * Return the alignment
172 * position for a sequence position
175 * lying from start to end
177 * @return aligned column for residue (0 if residue is upstream from
178 * alignment, -1 if residue is downstream from alignment) note.
179 * Sequence object returns sequence.getEnd() for positions upstream
180 * currently. TODO: change sequence for
181 * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
184 public int findIndex(int pos);
187 * Returns the sequence position for an alignment position
190 * column index in alignment (from 1)
192 * @return residue number for residue (left of and) nearest ith column
194 public int findPosition(int i);
197 * Returns an int array where indices correspond to each residue in the
198 * sequence and the element value gives its position in the alignment
200 * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
201 * residues in SequenceI object
203 public int[] gapMap();
206 * Returns an int array where indices correspond to each position in sequence
207 * char array and the element value gives the result of findPosition for that
208 * index in the sequence.
210 * @return int[SequenceI.getLength()]
212 public int[] findPositionMap();
215 * Delete a range of aligned sequence columns, creating a new dataset sequence
216 * if necessary and adjusting start and end positions accordingly.
219 * first column in range to delete
221 * last column in range to delete
223 public void deleteChars(int i, int j);
233 public void insertCharAt(int i, char c);
243 public void insertCharAt(int i, int length, char c);
248 * @return DOCUMENT ME!
250 public SequenceFeature[] getSequenceFeatures();
258 public void setSequenceFeatures(SequenceFeature[] features);
266 public void setPDBId(Vector ids);
271 * @return DOCUMENT ME!
273 public Vector getPDBId();
276 * add entry to the vector of PDBIds, if it isn't in the list already
280 public void addPDBId(PDBEntry entry);
283 * update the list of PDBEntrys to include any DBRefEntrys citing structural
286 * @return true if PDBEntry list was modified
288 public boolean updatePDBIds();
290 public String getVamsasId();
292 public void setVamsasId(String id);
294 public void setDBRef(DBRefEntry[] dbs);
296 public DBRefEntry[] getDBRef();
299 * add the given entry to the list of DBRefs for this sequence, or replace a
300 * similar one if entry contains a map object and the existing one doesnt.
304 public void addDBRef(DBRefEntry entry);
306 public void addSequenceFeature(SequenceFeature sf);
308 public void deleteFeature(SequenceFeature sf);
310 public void setDatasetSequence(SequenceI seq);
312 public SequenceI getDatasetSequence();
314 public AlignmentAnnotation[] getAnnotation();
316 public void addAlignmentAnnotation(AlignmentAnnotation annotation);
318 public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
321 * Derive a sequence (using this one's dataset or as the dataset)
323 * @return duplicate sequence with valid dataset sequence
325 public SequenceI deriveSequence();
328 * set the array of associated AlignmentAnnotation for this sequenceI
332 public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
335 * Get one or more alignment annotations with a particular label.
338 * string which each returned annotation must have as a label.
339 * @return null or array of annotations.
341 public AlignmentAnnotation[] getAnnotation(String label);
344 * create a new dataset sequence (if necessary) for this sequence and sets
345 * this sequence to refer to it. This call will move any features or
346 * references on the sequence onto the dataset.
348 * @return dataset sequence for this sequence
350 public SequenceI createDatasetSequence();
353 * Transfer any database references or annotation from entry under a sequence
358 * null or mapping from entry's numbering to local start/end
360 public void transferAnnotation(SequenceI entry, Mapping mp);
364 * The sequence index in the MSA
366 public void setIndex(int index);
369 * @return The index of the sequence in the alignment
371 public int getIndex();
374 * @return The RNA of the sequence in the alignment
380 * @param rna The RNA.
382 public void setRNA(RNA rna);