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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51 * @param start DOCUMENT ME!
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53 public void setStart(int start);
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58 * @return DOCUMENT ME!
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60 public int getStart();
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65 * @return DOCUMENT ME!
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67 public String getDisplayId();
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72 * @param end DOCUMENT ME!
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74 public void setEnd(int end);
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79 * @return DOCUMENT ME!
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81 public int getEnd();
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86 * @return DOCUMENT ME!
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88 public int getLength();
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93 * @param sequence DOCUMENT ME!
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95 public void setSequence(String sequence);
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100 * @return DOCUMENT ME!
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102 public String getSequence();
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107 * @param start DOCUMENT ME!
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108 * @param end DOCUMENT ME!
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110 * @return DOCUMENT ME!
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112 public String getSequence(int start, int end);
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117 * @param i DOCUMENT ME!
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119 * @return DOCUMENT ME!
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121 public char getCharAt(int i);
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126 * @param desc DOCUMENT ME!
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128 public void setDescription(String desc);
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133 * @return DOCUMENT ME!
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135 public String getDescription();
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140 * @param pos DOCUMENT ME!
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142 * @return DOCUMENT ME!
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144 public int findIndex(int pos);
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149 * @param i DOCUMENT ME!
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151 * @return DOCUMENT ME!
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153 public int findPosition(int i);
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158 * @return DOCUMENT ME!
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160 public int[] gapMap();
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165 * @param i DOCUMENT ME!
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166 * @param j DOCUMENT ME!
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168 public void deleteChars(int i, int j);
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173 * @param i DOCUMENT ME!
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175 public void deleteCharAt(int i);
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180 * @param i DOCUMENT ME!
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181 * @param c DOCUMENT ME!
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183 public void insertCharAt(int i, char c);
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188 * @param i DOCUMENT ME!
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189 * @param c DOCUMENT ME!
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190 * @param chop DOCUMENT ME!
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192 public void insertCharAt(int i, char c, boolean chop);
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197 * @param c DOCUMENT ME!
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199 public void setColor(Color c);
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204 * @return DOCUMENT ME!
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206 public Color getColor();
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211 * @return DOCUMENT ME!
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213 public Vector getSequenceFeatures();
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218 * @param v DOCUMENT ME!
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220 public void setSequenceFeatures(Vector v);
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225 * @param id DOCUMENT ME!
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227 public void setPDBId(String id);
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232 * @return DOCUMENT ME!
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234 public String getPDBId();
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