2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2005 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;
32 public interface SequenceI
37 * @param name DOCUMENT ME!
39 public void setName(String name);
44 * @return DOCUMENT ME!
46 public String getName();
52 * @param start DOCUMENT ME!
54 public void setStart(int start);
59 * @return DOCUMENT ME!
61 public int getStart();
66 * @return DOCUMENT ME!
68 public String getDisplayId(boolean jvsuffix);
73 * @param end DOCUMENT ME!
75 public void setEnd(int end);
80 * @return DOCUMENT ME!
87 * @return DOCUMENT ME!
89 public int getLength();
94 * @param sequence DOCUMENT ME!
96 public void setSequence(String sequence);
101 * @return DOCUMENT ME!
103 public String getSequence();
108 * @param start DOCUMENT ME!
109 * @param end DOCUMENT ME!
111 * @return DOCUMENT ME!
113 public String getSequence(int start, int end);
115 * create a new sequence object from start to end of this sequence
120 public SequenceI getSubSequence(int start, int end);
124 * @param i DOCUMENT ME!
126 * @return DOCUMENT ME!
128 public char getCharAt(int i);
133 * @param desc DOCUMENT ME!
135 public void setDescription(String desc);
140 * @return DOCUMENT ME!
142 public String getDescription();
147 * @param pos DOCUMENT ME!
149 * @return DOCUMENT ME!
151 public int findIndex(int pos);
156 * @param i DOCUMENT ME!
158 * @return DOCUMENT ME!
160 public int findPosition(int i);
165 * @return DOCUMENT ME!
167 public int[] gapMap();
172 * @param i DOCUMENT ME!
173 * @param j DOCUMENT ME!
175 public void deleteChars(int i, int j);
180 * @param i DOCUMENT ME!
182 public void deleteCharAt(int i);
187 * @param i DOCUMENT ME!
188 * @param c DOCUMENT ME!
190 public void insertCharAt(int i, char c);
196 * @param c DOCUMENT ME!
198 public void setColor(Color c);
203 * @return DOCUMENT ME!
205 public Color getColor();
210 * @return DOCUMENT ME!
212 public SequenceFeature[] getSequenceFeatures();
217 * @param v DOCUMENT ME!
219 public void setSequenceFeatures(SequenceFeature [] features);
224 * @param id DOCUMENT ME!
226 public void setPDBId(Vector ids);
231 * @return DOCUMENT ME!
233 public Vector getPDBId();
235 public void addPDBId(PDBEntry entry);
237 public String getVamsasId();
239 public void setVamsasId(String id);
241 public void setDBRef(DBRefEntry[] dbs);
243 public DBRefEntry [] getDBRef();
245 public void addDBRef(DBRefEntry entry);
247 public void addSequenceFeature(SequenceFeature sf);
249 public void setDatasetSequence(SequenceI seq);
251 public SequenceI getDatasetSequence();
253 public AlignmentAnnotation [] getAnnotation();
255 public void addAlignmentAnnotation(AlignmentAnnotation annotation);
257 public SequenceGroup getHiddenSequences();
259 public void addHiddenSequence(SequenceI seq);
261 public void showHiddenSequence(SequenceI seq);
263 public void changeCase(boolean toUpper, int start, int end);
265 public void toggleCase(int start, int end);
268 * getSubSequence from start to end of sequence
269 * @param start first residue in subSequence
272 public SequenceI getSubSequence(int start);
274 * remove all gaps in the sequence
275 * @return number of gaps removed
277 public int removeGaps();
279 * remove all gaps from start to end columns in sequence
282 * @return number of gaps removed
284 public int removeGaps(int start, int end);