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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21 import jalview.jbgui.*;
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25 import java.util.Vector;
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28 public interface SequenceI {
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29 public void setName(String name);
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31 public String getName();
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33 public void setStart(int start);
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35 public int getStart();
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37 public String getDisplayId();
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39 public void setEnd(int end);
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41 public int getEnd();
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43 public int getLength();
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45 public void setSequence(String sequence);
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47 public String getSequence();
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49 public String getSequence(int start, int end);
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51 public char getCharAt(int i);
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53 public void setDescription(String desc);
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55 public String getDescription();
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57 public int findIndex(int pos);
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59 public int findPosition(int i);
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61 public int[] gapMap();
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63 public void deleteChars(int i, int j);
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65 public void deleteCharAt(int i);
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67 public void insertCharAt(int i, char c);
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69 public void insertCharAt(int i, char c, boolean chop);
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71 public void setColor(Color c);
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73 public Color getColor();
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75 public Vector getSequenceFeatures();
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77 public void setSequenceFeatures(Vector v);
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79 public void setPDBId(String id);
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81 public String getPDBId();
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