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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23 import jalview.util.*;
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28 /** Data structure to hold and manipulate a multiple sequence alignment
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30 public class Alignment implements AlignmentI
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32 protected Alignment dataset;
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33 protected Vector sequences;
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34 protected Vector groups = new Vector();
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35 protected Vector superGroup = new Vector();
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36 protected char gapCharacter = '-';
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37 protected int type = NUCLEOTIDE;
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38 public static final int PROTEIN = 0;
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39 public static final int NUCLEOTIDE = 1;
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41 /** DOCUMENT ME!! */
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42 public AlignmentAnnotation[] annotations;
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44 /** Make an alignment from an array of Sequences.
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48 public Alignment(SequenceI[] seqs)
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52 if( jalview.util.Comparison.isNucleotide(seqs))
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57 sequences = new Vector();
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59 for (i = 0; i < seqs.length; i++)
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61 sequences.addElement(seqs[i]);
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70 * @return DOCUMENT ME!
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72 public Vector getSequences()
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80 * @param i DOCUMENT ME!
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82 * @return DOCUMENT ME!
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84 public SequenceI getSequenceAt(int i)
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86 if (i < sequences.size())
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88 return (SequenceI) sequences.elementAt(i);
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94 /** Adds a sequence to the alignment. Recalculates maxLength and size.
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98 public void addSequence(SequenceI snew)
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100 sequences.addElement(snew);
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106 * @param seq DOCUMENT ME!
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108 public void addSequence(SequenceI[] seq)
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110 for (int i = 0; i < seq.length; i++)
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112 addSequence(seq[i]);
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116 /** Adds a sequence to the alignment. Recalculates maxLength and size.
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120 public void setSequenceAt(int i, SequenceI snew)
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122 SequenceI oldseq = getSequenceAt(i);
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123 deleteSequence(oldseq);
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125 sequences.setElementAt(snew, i);
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131 * @return DOCUMENT ME!
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133 public Vector getGroups()
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138 /** Takes out columns consisting entirely of gaps (-,.," ")
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140 public void removeGaps()
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143 int iSize = getWidth();
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145 for (int i = 0; i < iSize; i++)
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147 boolean delete = true;
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149 for (int j = 0; j < getHeight(); j++)
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151 current = getSequenceAt(j);
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153 if (current.getLength() > i)
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155 /* MC Should move this to a method somewhere */
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156 if (!jalview.util.Comparison.isGap(current.getCharAt(i)))
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165 deleteColumns(i, i);
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172 /** Removes a range of columns (start to end inclusive).
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174 * @param start Start column in the alignment
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175 * @param end End column in the alignment
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177 public void deleteColumns(int start, int end)
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179 deleteColumns(0, getHeight() - 1, start, end);
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185 * @param seq1 DOCUMENT ME!
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186 * @param seq2 DOCUMENT ME!
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187 * @param start DOCUMENT ME!
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188 * @param end DOCUMENT ME!
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190 public void deleteColumns(int seq1, int seq2, int start, int end)
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192 for (int i = 0; i <= (end - start); i++)
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194 for (int j = seq1; j <= seq2; j++)
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196 getSequenceAt(j).deleteCharAt(start);
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204 * @param i DOCUMENT ME!
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206 public void trimLeft(int i)
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208 for (int j = 0; j < getHeight(); j++)
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210 SequenceI s = getSequenceAt(j);
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211 int newstart = s.findPosition(i);
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213 s.setStart(newstart);
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214 s.setSequence(s.getSequence().substring(i));
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221 * @param i DOCUMENT ME!
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223 public void trimRight(int i)
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225 for (int j = 0; j < getHeight(); j++)
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227 SequenceI s = getSequenceAt(j);
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228 int newend = s.findPosition(i);
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231 s.setSequence(s.getSequence().substring(0, i + 1));
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238 * @param s DOCUMENT ME!
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240 public void deleteSequence(SequenceI s)
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242 for (int i = 0; i < getHeight(); i++)
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244 if (getSequenceAt(i) == s)
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254 * @param i DOCUMENT ME!
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256 public void deleteSequence(int i)
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258 sequences.removeElementAt(i);
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264 * @param threshold DOCUMENT ME!
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265 * @param sel DOCUMENT ME!
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267 * @return DOCUMENT ME!
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269 public Vector removeRedundancy(float threshold, Vector sel)
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271 Vector del = new Vector();
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273 for (int i = 1; i < sel.size(); i++)
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275 for (int j = 0; j < i; j++)
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277 // Only do the comparison if either have not been deleted
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278 if (!del.contains((SequenceI) sel.elementAt(i)) ||
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279 !del.contains((SequenceI) sel.elementAt(j)))
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281 // use PID instead of Comparison (which is really not pleasant)
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282 float pid = Comparison.PID((SequenceI) sel.elementAt(j),
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283 (SequenceI) sel.elementAt(i));
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285 if (pid >= threshold)
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287 // Delete the shortest one
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288 if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel
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290 i)).getSequence().length())
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292 del.addElement(sel.elementAt(i));
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296 del.addElement(sel.elementAt(i));
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303 // Now delete the sequences
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304 for (int i = 0; i < del.size(); i++)
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306 deleteSequence((SequenceI) del.elementAt(i));
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313 public SequenceGroup findGroup(int i)
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315 return findGroup(getSequenceAt(i));
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319 public SequenceGroup findGroup(SequenceI s)
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321 for (int i = 0; i < this.groups.size(); i++)
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323 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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325 if (sg.sequences.contains(s))
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337 * @param s DOCUMENT ME!
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339 * @return DOCUMENT ME!
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341 public SequenceGroup[] findAllGroups(SequenceI s)
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343 Vector temp = new Vector();
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345 int gSize = groups.size();
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346 for (int i = 0; i < gSize; i++)
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348 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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349 if(sg==null || sg.sequences==null)
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351 this.deleteGroup(sg);
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356 if (sg.sequences.contains(s))
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358 temp.addElement(sg);
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362 SequenceGroup[] ret = new SequenceGroup[temp.size()];
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364 for (int i = 0; i < temp.size(); i++)
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366 ret[i] = (SequenceGroup) temp.elementAt(i);
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375 * @param sg DOCUMENT ME!
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377 public void addSuperGroup(SuperGroup sg)
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379 superGroup.addElement(sg);
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385 * @param sg DOCUMENT ME!
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387 public void removeSuperGroup(SuperGroup sg)
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389 superGroup.removeElement(sg);
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395 * @param sg DOCUMENT ME!
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397 * @return DOCUMENT ME!
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399 public SuperGroup getSuperGroup(SequenceGroup sg)
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401 for (int i = 0; i < this.superGroup.size(); i++)
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403 SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
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405 if (temp.sequenceGroups.contains(sg))
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415 public void addGroup(SequenceGroup sg)
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417 if (!groups.contains(sg))
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419 groups.addElement(sg);
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426 public void deleteAllGroups()
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428 groups.removeAllElements();
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429 superGroup.removeAllElements();
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433 while (i < sequences.size())
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435 SequenceI s = getSequenceAt(i);
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436 s.setColor(java.awt.Color.white);
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442 public void deleteGroup(SequenceGroup g)
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444 if (groups.contains(g))
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446 groups.removeElement(g);
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451 public SequenceI findName(String name)
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455 while (i < sequences.size())
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457 if (getSequenceAt(i).getName().equals(name))
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459 return getSequenceAt(i);
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470 public int findIndex(SequenceI s)
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474 while (i < sequences.size())
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476 if (s == getSequenceAt(i))
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490 * @return DOCUMENT ME!
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492 public int getHeight()
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494 return sequences.size();
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500 * @return DOCUMENT ME!
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502 public int getWidth()
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504 int maxLength = -1;
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506 for (int i = 0; i < sequences.size(); i++)
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508 if (getSequenceAt(i).getLength() > maxLength)
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510 maxLength = getSequenceAt(i).getLength();
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520 * @return DOCUMENT ME!
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522 public int getMaxIdLength()
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527 while (i < sequences.size())
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529 SequenceI seq = getSequenceAt(i);
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530 String tmp = seq.getName() + "/" + seq.getStart() + "-" +
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533 if (tmp.length() > max)
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535 max = tmp.length();
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547 * @param gc DOCUMENT ME!
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549 public void setGapCharacter(char gc)
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553 for (int i = 0; i < sequences.size(); i++)
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555 Sequence seq = (Sequence) sequences.elementAt(i);
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556 seq.sequence = seq.sequence.replace('.', gc);
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557 seq.sequence = seq.sequence.replace('-', gc);
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558 seq.sequence = seq.sequence.replace(' ', gc);
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565 * @return DOCUMENT ME!
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567 public char getGapCharacter()
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569 return gapCharacter;
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575 * @return DOCUMENT ME!
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577 public Vector getAAFrequency()
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579 return AAFrequency.calculate(sequences, 0, getWidth());
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585 * @return DOCUMENT ME!
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587 public boolean isAligned()
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589 int width = getWidth();
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591 for (int i = 0; i < sequences.size(); i++)
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593 if (getSequenceAt(i).getLength() != width)
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605 * @param aa DOCUMENT ME!
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607 public void deleteAnnotation(AlignmentAnnotation aa)
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611 if (annotations != null)
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613 aSize = annotations.length;
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616 AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
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620 for (int i = 0; i < aSize; i++)
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622 if (annotations[i] == aa)
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627 temp[tIndex] = annotations[i];
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631 annotations = temp;
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637 * @param aa DOCUMENT ME!
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639 public void addAnnotation(AlignmentAnnotation aa)
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643 if (annotations != null)
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645 aSize = annotations.length + 1;
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649 AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
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654 for (i = 0; i < (aSize - 1); i++)
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656 temp[i] = annotations[i];
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662 annotations = temp;
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668 * @return DOCUMENT ME!
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670 public AlignmentAnnotation[] getAlignmentAnnotation()
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672 return annotations;
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675 public void setNucleotide(boolean b)
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683 public boolean isNucleotide()
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685 if(type==NUCLEOTIDE)
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691 public void setDataset(Alignment data)
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693 if(dataset==null && data==null)
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695 // Create a new dataset for this alignment.
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696 // Can only be done once, if dataset is not null
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697 // This will not be performed
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698 Sequence[] seqs = new Sequence[getHeight()];
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699 for (int i = 0; i < getHeight(); i++)
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702 seqs[i] = new Sequence(getSequenceAt(i).getName(),
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703 AlignSeq.extractGaps(
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704 jalview.util.Comparison.GapChars,
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705 getSequenceAt(i).getSequence()
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707 getSequenceAt(i).getStart(),
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708 getSequenceAt(i).getEnd());
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710 getSequenceAt(i).setDatasetSequence(seqs[i]);
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713 dataset = new Alignment(seqs);
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715 else if(dataset==null && data!=null)
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721 public Alignment getDataset()
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