2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.datamodel;
30 public interface SequenceI
35 * @param name DOCUMENT ME!
37 public void setName(String name);
42 * @return DOCUMENT ME!
44 public String getName();
50 * @param start DOCUMENT ME!
52 public void setStart(int start);
57 * @return DOCUMENT ME!
59 public int getStart();
64 * @return DOCUMENT ME!
66 public String getDisplayId(boolean jvsuffix);
71 * @param end DOCUMENT ME!
73 public void setEnd(int end);
78 * @return DOCUMENT ME!
85 * @return DOCUMENT ME!
87 public int getLength();
92 * @param sequence DOCUMENT ME!
94 public void setSequence(String sequence);
99 * @return DOCUMENT ME!
101 public String getSequenceAsString();
106 * @param start DOCUMENT ME!
107 * @param end DOCUMENT ME!
109 * @return DOCUMENT ME!
111 public String getSequenceAsString(int start, int end);
116 * @return DOCUMENT ME!
118 public char [] getSequence();
123 * @param start DOCUMENT ME!
124 * @param end DOCUMENT ME!
126 * @return DOCUMENT ME!
128 public char [] getSequence(int start, int end);
130 * create a new sequence object from start to end of this sequence
135 public SequenceI getSubSequence(int start, int end);
139 * @param i DOCUMENT ME!
141 * @return DOCUMENT ME!
143 public char getCharAt(int i);
148 * @param desc DOCUMENT ME!
150 public void setDescription(String desc);
155 * @return DOCUMENT ME!
157 public String getDescription();
162 * @param pos DOCUMENT ME!
164 * @return DOCUMENT ME!
166 public int findIndex(int pos);
169 * Returns the sequence position for an alignment position
171 * @param i column index in alignment (from 1)
173 * @return residue number for residue (left of and) nearest ith column
175 public int findPosition(int i);
178 * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
180 * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
182 public int[] gapMap();
187 * @param i DOCUMENT ME!
188 * @param j DOCUMENT ME!
190 public void deleteChars(int i, int j);
196 * @param i DOCUMENT ME!
197 * @param c DOCUMENT ME!
199 public void insertCharAt(int i, char c);
204 * @param i DOCUMENT ME!
205 * @param c DOCUMENT ME!
207 public void insertCharAt(int i, int length, char c);
213 * @return DOCUMENT ME!
215 public SequenceFeature[] getSequenceFeatures();
220 * @param v DOCUMENT ME!
222 public void setSequenceFeatures(SequenceFeature [] features);
227 * @param id DOCUMENT ME!
229 public void setPDBId(Vector ids);
234 * @return DOCUMENT ME!
236 public Vector getPDBId();
238 public void addPDBId(PDBEntry entry);
240 public String getVamsasId();
242 public void setVamsasId(String id);
244 public void setDBRef(DBRefEntry[] dbs);
246 public DBRefEntry [] getDBRef();
248 public void addDBRef(DBRefEntry entry);
250 public void addSequenceFeature(SequenceFeature sf);
252 public void deleteFeature(SequenceFeature sf);
254 public void setDatasetSequence(SequenceI seq);
256 public SequenceI getDatasetSequence();
258 public AlignmentAnnotation [] getAnnotation();
260 public void addAlignmentAnnotation(AlignmentAnnotation annotation);
264 * Derive a sequence (using this one's dataset or as the dataset)
265 * @return duplicate sequence with valid dataset sequence
267 public SequenceI deriveSequence();