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.analysis.*;
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32 * @version $Revision$
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34 public class Sequence implements SequenceI
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36 protected String name;
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37 protected String sequence;
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38 protected String description;
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39 protected int start;
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41 protected String displayId;
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42 protected Color color = Color.white;
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45 /** DOCUMENT ME!! */
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46 public Vector sequenceFeatures = new Vector();
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49 * Creates a new Sequence object.
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51 * @param name DOCUMENT ME!
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52 * @param sequence DOCUMENT ME!
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53 * @param start DOCUMENT ME!
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54 * @param end DOCUMENT ME!
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56 public Sequence(String name, String sequence, int start, int end)
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59 this.sequence = sequence;
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67 for (int j = 0; j < sequence.length(); j++)
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69 ch = sequence.charAt(j);
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70 if (!jalview.util.Comparison.isGap( (ch)))
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77 endRes += start - 1;
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87 * Creates a new Sequence object.
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89 * @param name DOCUMENT ME!
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90 * @param sequence DOCUMENT ME!
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92 public Sequence(String name, String sequence)
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94 this(name, sequence, 1, sequence.length());
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98 * Creates a new Sequence object.
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100 * @param seq DOCUMENT ME!
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102 public Sequence(SequenceI seq)
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104 this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
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110 * @param v DOCUMENT ME!
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112 public void setSequenceFeatures(Vector v)
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114 sequenceFeatures = v;
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120 * @return DOCUMENT ME!
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122 public Vector getSequenceFeatures()
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124 return sequenceFeatures;
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130 * @param id DOCUMENT ME!
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132 public void setPDBId(String id)
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140 * @return DOCUMENT ME!
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142 public String getPDBId()
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150 * @return DOCUMENT ME!
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152 public String getDisplayId()
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160 public void setDisplayId()
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162 displayId = name + "/" + start + "-" + end;
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168 * @param name DOCUMENT ME!
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170 public void setName(String name)
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179 * @return DOCUMENT ME!
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181 public String getName()
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189 * @param start DOCUMENT ME!
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191 public void setStart(int start)
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193 this.start = start;
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200 * @return DOCUMENT ME!
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202 public int getStart()
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210 * @param end DOCUMENT ME!
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212 public void setEnd(int end)
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221 * @return DOCUMENT ME!
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223 public int getEnd()
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231 * @return DOCUMENT ME!
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233 public int getLength()
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235 return this.sequence.length();
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241 * @param seq DOCUMENT ME!
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243 public void setSequence(String seq)
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245 this.sequence = seq;
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251 * @return DOCUMENT ME!
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253 public String getSequence()
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255 return this.sequence;
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261 * @param start DOCUMENT ME!
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262 * @param end DOCUMENT ME!
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264 * @return DOCUMENT ME!
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266 public String getSequence(int start, int end)
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268 // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
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269 if (start >= sequence.length())
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274 if (end >= sequence.length())
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276 end = sequence.length();
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279 return this.sequence.substring(start, end);
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285 * @param i DOCUMENT ME!
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287 * @return DOCUMENT ME!
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289 public char getCharAt(int i)
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291 if (i < sequence.length())
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293 return sequence.charAt(i);
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304 * @param desc DOCUMENT ME!
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306 public void setDescription(String desc)
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308 this.description = desc;
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314 * @return DOCUMENT ME!
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316 public String getDescription()
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318 return this.description;
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324 * @param pos DOCUMENT ME!
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326 * @return DOCUMENT ME!
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328 public int findIndex(int pos)
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330 // returns the alignment position for a residue
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334 while ((i < sequence.length()) && (j <= end) && (j <= pos))
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336 char c = sequence.charAt(i);
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338 if (!jalview.util.Comparison.isGap((c)))
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346 if ((j == end) && (j < pos))
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359 * @param i DOCUMENT ME!
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361 * @return DOCUMENT ME!
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363 public int findPosition(int i)
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365 // Returns the sequence position for an alignment position
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369 while ((j < i) && (j < sequence.length()))
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371 char c = sequence.charAt(j);
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373 if (!jalview.util.Comparison.isGap((c)))
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387 * @return DOCUMENT ME!
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389 public int[] gapMap()
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391 // Returns an int array giving the position of each residue in the sequence in the alignment
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392 String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);
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393 int[] map = new int[seq.length()];
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397 while (j < sequence.length())
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399 if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
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413 * @param i DOCUMENT ME!
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415 public void deleteCharAt(int i)
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417 if (i >= sequence.length())
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422 sequence = sequence.substring(0, i) + sequence.substring(i + 1);
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428 * @param i DOCUMENT ME!
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429 * @param j DOCUMENT ME!
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431 public void deleteChars(int i, int j)
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433 if (i >= sequence.length())
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438 if (j >= sequence.length())
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440 sequence = sequence.substring(0, i);
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444 sequence = sequence.substring(0, i) + sequence.substring(j);
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451 * @param i DOCUMENT ME!
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452 * @param c DOCUMENT ME!
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454 public void insertCharAt(int i, char c)
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456 insertCharAt(i, c, true);
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462 * @param i DOCUMENT ME!
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463 * @param c DOCUMENT ME!
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464 * @param chop DOCUMENT ME!
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466 public void insertCharAt(int i, char c, boolean chop)
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468 String tmp = new String(sequence);
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470 if (i < sequence.length())
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472 sequence = tmp.substring(0, i) + String.valueOf(c) +
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477 // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!
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478 char[] ch = new char[(1 + i) - sequence.length()];
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480 for (int j = 0, k = ch.length; j < k; j++)
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483 sequence = tmp + String.valueOf(ch);
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490 * @param c DOCUMENT ME!
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492 public void setColor(Color c)
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500 * @return DOCUMENT ME!
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502 public Color getColor()
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