2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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/>.
18 package jalview.datamodel;
20 import java.util.Vector;
28 public interface SequenceI
31 * Set the display name for the sequence
35 public void setName(String name);
38 * Get the display name
40 public String getName();
43 * Set start position of first non-gapped symbol in sequence
48 public void setStart(int start);
51 * get start position of first non-gapped residue in sequence
55 public int getStart();
58 * get the displayed id of the sequence
60 * @return true means the id will be returned in the form
61 * DisplayName/Start-End
63 public String getDisplayId(boolean jvsuffix);
66 * set end position for last residue in sequence
70 public void setEnd(int end);
73 * get end position for last residue in sequence getEnd()>getStart() unless
74 * sequence only consists of gap characters
81 * @return length of sequence including gaps
84 public int getLength();
87 * Replace the sequence with the given string
92 public void setSequence(String sequence);
95 * @return sequence as string
97 public String getSequenceAsString();
100 * get a range on the seuqence as a string
107 * @return DOCUMENT ME!
109 public String getSequenceAsString(int start, int end);
114 * @return DOCUMENT ME!
116 public char[] getSequence();
119 * get stretch of sequence characters in an array
122 * absolute index into getSequence()
124 * exclusive index of last position in segment to be returned.
126 * @return char[max(0,end-start)];
128 public char[] getSequence(int start, int end);
131 * create a new sequence object from start to end of this sequence
139 public SequenceI getSubSequence(int start, int end);
147 * @return DOCUMENT ME!
149 public char getCharAt(int i);
157 public void setDescription(String desc);
162 * @return DOCUMENT ME!
164 public String getDescription();
167 * Return the alignment column for a sequence position
168 * * Return the alignment position for a sequence position
171 * lying from start to end
173 * @return aligned column for residue (0 if residue is upstream from alignment, -1 if residue is downstream from alignment)
174 * note. Sequence object returns sequence.getEnd() for positions upstream currently. TODO: change sequence for assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
177 public int findIndex(int pos);
180 * Returns the sequence position for an alignment position
183 * column index in alignment (from 1)
185 * @return residue number for residue (left of and) nearest ith column
187 public int findPosition(int i);
190 * Returns an int array where indices correspond to each residue in the
191 * sequence and the element value gives its position in the alignment
193 * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
194 * residues in SequenceI object
196 public int[] gapMap();
199 * Returns an int array where indices correspond to each position in sequence
200 * char array and the element value gives the result of findPosition for that
201 * index in the sequence.
203 * @return int[SequenceI.getLength()]
205 public int[] findPositionMap();
208 * Delete a range of aligned sequence columns, creating a new dataset sequence
209 * if necessary and adjusting start and end positions accordingly.
212 * first column in range to delete
214 * last column in range to delete
216 public void deleteChars(int i, int j);
226 public void insertCharAt(int i, char c);
236 public void insertCharAt(int i, int length, char c);
241 * @return DOCUMENT ME!
243 public SequenceFeature[] getSequenceFeatures();
251 public void setSequenceFeatures(SequenceFeature[] features);
259 public void setPDBId(Vector ids);
264 * @return DOCUMENT ME!
266 public Vector getPDBId();
269 * add entry to the vector of PDBIds, if it isn't in the list already
273 public void addPDBId(PDBEntry entry);
276 * update the list of PDBEntrys to include any DBRefEntrys citing structural
279 * @return true if PDBEntry list was modified
281 public boolean updatePDBIds();
283 public String getVamsasId();
285 public void setVamsasId(String id);
287 public void setDBRef(DBRefEntry[] dbs);
289 public DBRefEntry[] getDBRef();
292 * add the given entry to the list of DBRefs for this sequence, or replace a
293 * similar one if entry contains a map object and the existing one doesnt.
297 public void addDBRef(DBRefEntry entry);
299 public void addSequenceFeature(SequenceFeature sf);
301 public void deleteFeature(SequenceFeature sf);
303 public void setDatasetSequence(SequenceI seq);
305 public SequenceI getDatasetSequence();
307 public AlignmentAnnotation[] getAnnotation();
309 public void addAlignmentAnnotation(AlignmentAnnotation annotation);
311 public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
314 * Derive a sequence (using this one's dataset or as the dataset)
316 * @return duplicate sequence with valid dataset sequence
318 public SequenceI deriveSequence();
321 * set the array of associated AlignmentAnnotation for this sequenceI
325 public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
328 * Get one or more alignment annotations with a particular label.
331 * string which each returned annotation must have as a label.
332 * @return null or array of annotations.
334 public AlignmentAnnotation[] getAnnotation(String label);
337 * create a new dataset sequence (if necessary) for this sequence and sets
338 * this sequence to refer to it. This call will move any features or
339 * references on the sequence onto the dataset.
341 * @return dataset sequence for this sequence
343 public SequenceI createDatasetSequence();
346 * Transfer any database references or annotation from entry under a sequence
351 * null or mapping from entry's numbering to local start/end
353 public void transferAnnotation(SequenceI entry, Mapping mp);
356 * @param index The sequence index in the MSA
358 public void setIndex(int index);
361 * @return The index of the sequence in the alignment
363 public int getIndex();