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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23 import jalview.analysis.*;
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34 * @version $Revision$
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36 public class Sequence implements SequenceI
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38 protected String name;
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39 protected String sequence;
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40 protected String description;
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41 protected int start;
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43 protected String displayId;
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44 protected Color color = Color.white;
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47 /** DOCUMENT ME!! */
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48 public Vector sequenceFeatures = new Vector();
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51 * Creates a new Sequence object.
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53 * @param name DOCUMENT ME!
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54 * @param sequence DOCUMENT ME!
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55 * @param start DOCUMENT ME!
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56 * @param end DOCUMENT ME!
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58 public Sequence(String name, String sequence, int start, int end)
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61 this.sequence = sequence;
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69 * Creates a new Sequence object.
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71 * @param name DOCUMENT ME!
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72 * @param sequence DOCUMENT ME!
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74 public Sequence(String name, String sequence)
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76 this(name, sequence, 1, sequence.length());
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80 * Creates a new Sequence object.
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82 * @param seq DOCUMENT ME!
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84 public Sequence(SequenceI seq)
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86 this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
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92 * @param v DOCUMENT ME!
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94 public void setSequenceFeatures(Vector v)
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96 sequenceFeatures = v;
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102 * @return DOCUMENT ME!
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104 public Vector getSequenceFeatures()
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106 return sequenceFeatures;
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112 * @param id DOCUMENT ME!
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114 public void setPDBId(String id)
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122 * @return DOCUMENT ME!
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124 public String getPDBId()
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132 * @return DOCUMENT ME!
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134 public String getDisplayId()
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142 public void setDisplayId()
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144 displayId = name + "/" + start + "-" + end;
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150 * @param name DOCUMENT ME!
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152 public void setName(String name)
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161 * @return DOCUMENT ME!
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163 public String getName()
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171 * @param start DOCUMENT ME!
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173 public void setStart(int start)
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175 this.start = start;
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182 * @return DOCUMENT ME!
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184 public int getStart()
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192 * @param end DOCUMENT ME!
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194 public void setEnd(int end)
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203 * @return DOCUMENT ME!
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205 public int getEnd()
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213 * @return DOCUMENT ME!
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215 public int getLength()
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217 return this.sequence.length();
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223 * @param seq DOCUMENT ME!
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225 public void setSequence(String seq)
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227 this.sequence = seq;
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233 * @return DOCUMENT ME!
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235 public String getSequence()
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237 return this.sequence;
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243 * @param start DOCUMENT ME!
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244 * @param end DOCUMENT ME!
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246 * @return DOCUMENT ME!
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248 public String getSequence(int start, int end)
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250 // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
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251 if (start >= sequence.length())
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256 if (end >= sequence.length())
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258 end = sequence.length();
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261 return this.sequence.substring(start, end);
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267 * @param i DOCUMENT ME!
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269 * @return DOCUMENT ME!
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271 public char getCharAt(int i)
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273 if (i < sequence.length())
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275 return sequence.charAt(i);
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286 * @param desc DOCUMENT ME!
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288 public void setDescription(String desc)
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290 this.description = desc;
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296 * @return DOCUMENT ME!
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298 public String getDescription()
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300 return this.description;
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306 * @param pos DOCUMENT ME!
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308 * @return DOCUMENT ME!
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310 public int findIndex(int pos)
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312 // returns the alignment position for a residue
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316 while ((i < sequence.length()) && (j <= end) && (j <= pos))
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318 char c = sequence.charAt(i);
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320 if (!jalview.util.Comparison.isGap((c)))
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328 if ((j == end) && (j < pos))
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341 * @param i DOCUMENT ME!
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343 * @return DOCUMENT ME!
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345 public int findPosition(int i)
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347 // Returns the sequence position for an alignment position
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351 while ((j < i) && (j < sequence.length()))
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353 char c = sequence.charAt(j);
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355 if (!jalview.util.Comparison.isGap((c)))
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369 * @return DOCUMENT ME!
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371 public int[] gapMap()
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373 // Returns an int array giving the position of each residue in the sequence in the alignment
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374 String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);
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375 int[] map = new int[seq.length()];
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379 while (j < sequence.length())
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381 if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
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395 * @param i DOCUMENT ME!
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397 public void deleteCharAt(int i)
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399 if (i >= sequence.length())
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404 sequence = sequence.substring(0, i) + sequence.substring(i + 1);
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410 * @param i DOCUMENT ME!
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411 * @param j DOCUMENT ME!
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413 public void deleteChars(int i, int j)
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415 if (i >= sequence.length())
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420 if (j >= sequence.length())
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422 sequence = sequence.substring(0, i);
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426 sequence = sequence.substring(0, i) + sequence.substring(j);
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433 * @param i DOCUMENT ME!
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434 * @param c DOCUMENT ME!
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436 public void insertCharAt(int i, char c)
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438 insertCharAt(i, c, true);
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444 * @param i DOCUMENT ME!
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445 * @param c DOCUMENT ME!
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446 * @param chop DOCUMENT ME!
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448 public void insertCharAt(int i, char c, boolean chop)
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450 String tmp = new String(sequence);
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452 if (i < sequence.length())
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454 sequence = tmp.substring(0, i) + String.valueOf(c) +
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459 // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!
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460 char[] ch = new char[(1 + i) - sequence.length()];
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462 for (int j = 0, k = ch.length; j < k; j++)
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465 sequence = tmp + String.valueOf(ch);
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472 * @param c DOCUMENT ME!
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474 public void setColor(Color c)
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482 * @return DOCUMENT ME!
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484 public Color getColor()
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