2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.datamodel;
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30 * @version $Revision$
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32 public interface SequenceI
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37 * @param name DOCUMENT ME!
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39 public void setName(String name);
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44 * @return DOCUMENT ME!
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46 public String getName();
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52 * @param start DOCUMENT ME!
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54 public void setStart(int start);
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59 * @return DOCUMENT ME!
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61 public int getStart();
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66 * @return DOCUMENT ME!
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68 public String getDisplayId(boolean jvsuffix);
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73 * @param end DOCUMENT ME!
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75 public void setEnd(int end);
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80 * @return DOCUMENT ME!
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82 public int getEnd();
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87 * @return DOCUMENT ME!
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89 public int getLength();
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94 * @param sequence DOCUMENT ME!
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96 public void setSequence(String sequence);
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101 * @return DOCUMENT ME!
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103 public String getSequence();
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108 * @param start DOCUMENT ME!
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109 * @param end DOCUMENT ME!
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111 * @return DOCUMENT ME!
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113 public String getSequence(int start, int end);
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115 * create a new sequence object from start to end of this sequence
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118 * @return SequenceI
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120 public SequenceI getSubSequence(int start, int end);
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124 * @param i DOCUMENT ME!
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126 * @return DOCUMENT ME!
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128 public char getCharAt(int i);
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133 * @param desc DOCUMENT ME!
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135 public void setDescription(String desc);
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140 * @return DOCUMENT ME!
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142 public String getDescription();
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147 * @param pos DOCUMENT ME!
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149 * @return DOCUMENT ME!
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151 public int findIndex(int pos);
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156 * @param i DOCUMENT ME!
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158 * @return DOCUMENT ME!
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160 public int findPosition(int i);
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165 * @return DOCUMENT ME!
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167 public int[] gapMap();
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172 * @param i DOCUMENT ME!
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173 * @param j DOCUMENT ME!
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175 public void deleteChars(int i, int j);
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180 * @param i DOCUMENT ME!
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182 public void deleteCharAt(int i);
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187 * @param i DOCUMENT ME!
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188 * @param c DOCUMENT ME!
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190 public void insertCharAt(int i, char c);
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196 * @param c DOCUMENT ME!
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198 public void setColor(Color c);
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203 * @return DOCUMENT ME!
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205 public Color getColor();
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210 * @return DOCUMENT ME!
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212 public SequenceFeature[] getSequenceFeatures();
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217 * @param v DOCUMENT ME!
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219 public void setSequenceFeatures(SequenceFeature [] features);
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224 * @param id DOCUMENT ME!
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226 public void setPDBId(Vector ids);
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231 * @return DOCUMENT ME!
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233 public Vector getPDBId();
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235 public void addPDBId(PDBEntry entry);
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237 public String getVamsasId();
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239 public void setVamsasId(String id);
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241 public void setDBRef(DBRefEntry[] dbs);
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243 public DBRefEntry [] getDBRef();
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245 public void addDBRef(DBRefEntry entry);
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247 public void addSequenceFeature(SequenceFeature sf);
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249 public void setDatasetSequence(SequenceI seq);
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251 public SequenceI getDatasetSequence();
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253 public AlignmentAnnotation [] getAnnotation();
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255 public void addAlignmentAnnotation(AlignmentAnnotation annotation);
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257 public SequenceGroup getHiddenSequences();
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259 public void addHiddenSequence(SequenceI seq);
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261 public void showHiddenSequence(SequenceI seq);
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263 public void changeCase(boolean toUpper, int start, int end);
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265 public void toggleCase(int start, int end);
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268 * getSubSequence from start to end of sequence
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269 * @param start first residue in subSequence
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270 * @return SequenceI
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272 public SequenceI getSubSequence(int start);
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