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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63 if(seqs[i].getDatasetSequence()!=null
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64 && seqs[i].getDatasetSequence().getAnnotation()!=null)
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67 for(int a=0; a<seqs[i].getDatasetSequence().getAnnotation().length; a++)
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69 this.addAnnotation(seqs[i].getDatasetSequence().getAnnotation()[a], seqs[i]);
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80 * @return DOCUMENT ME!
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82 public Vector getSequences()
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90 * @param i DOCUMENT ME!
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92 * @return DOCUMENT ME!
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94 public SequenceI getSequenceAt(int i)
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96 if (i < sequences.size())
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98 return (SequenceI) sequences.elementAt(i);
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104 /** Adds a sequence to the alignment. Recalculates maxLength and size.
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108 public void addSequence(SequenceI snew)
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110 sequences.addElement(snew);
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116 * @param seq DOCUMENT ME!
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118 public void addSequence(SequenceI[] seq)
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120 for (int i = 0; i < seq.length; i++)
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122 addSequence(seq[i]);
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126 /** Adds a sequence to the alignment. Recalculates maxLength and size.
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130 public void setSequenceAt(int i, SequenceI snew)
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132 SequenceI oldseq = getSequenceAt(i);
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133 deleteSequence(oldseq);
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135 sequences.setElementAt(snew, i);
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141 * @return DOCUMENT ME!
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143 public Vector getGroups()
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148 /** Takes out columns consisting entirely of gaps (-,.," ")
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150 public void removeGaps()
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153 int iSize = getWidth();
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155 for (int i = 0; i < iSize; i++)
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157 boolean delete = true;
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159 for (int j = 0; j < getHeight(); j++)
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161 current = getSequenceAt(j);
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163 if (current.getLength() > i)
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165 /* MC Should move this to a method somewhere */
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166 if (!jalview.util.Comparison.isGap(current.getCharAt(i)))
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175 deleteColumns(i, i);
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182 /** Removes a range of columns (start to end inclusive).
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184 * @param start Start column in the alignment
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185 * @param end End column in the alignment
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187 public void deleteColumns(int start, int end)
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189 deleteColumns(0, getHeight() - 1, start, end);
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195 * @param seq1 DOCUMENT ME!
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196 * @param seq2 DOCUMENT ME!
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197 * @param start DOCUMENT ME!
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198 * @param end DOCUMENT ME!
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200 public void deleteColumns(int seq1, int seq2, int start, int end)
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202 for (int i = 0; i <= (end - start); i++)
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204 for (int j = seq1; j <= seq2; j++)
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206 getSequenceAt(j).deleteCharAt(start);
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214 * @param i DOCUMENT ME!
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216 public void trimLeft(int i)
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218 int j, jSize = getHeight();
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219 for (j = 0; j < jSize; j++)
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221 SequenceI s = getSequenceAt(j);
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222 int newstart = s.findPosition(i);
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224 if(i>s.getLength())
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226 sequences.removeElement(s);
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232 s.setStart(newstart);
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233 s.setSequence(s.getSequence().substring(i));
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241 * @param i DOCUMENT ME!
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243 public void trimRight(int i)
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245 for (int j = 0; j < getHeight(); j++)
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247 SequenceI s = getSequenceAt(j);
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248 int newend = s.findPosition(i);
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251 if(s.getLength()>i)
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252 s.setSequence(s.getSequence().substring(0, i + 1));
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259 * @param s DOCUMENT ME!
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261 public void deleteSequence(SequenceI s)
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263 for (int i = 0; i < getHeight(); i++)
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265 if (getSequenceAt(i) == s)
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275 * @param i DOCUMENT ME!
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277 public void deleteSequence(int i)
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279 sequences.removeElementAt(i);
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285 * @param threshold DOCUMENT ME!
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286 * @param sel DOCUMENT ME!
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288 * @return DOCUMENT ME!
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290 public Vector removeRedundancy(float threshold, Vector sel)
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292 Vector del = new Vector();
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294 for (int i = 1; i < sel.size(); i++)
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296 for (int j = 0; j < i; j++)
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298 // Only do the comparison if either have not been deleted
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299 if (!del.contains((SequenceI) sel.elementAt(i)) ||
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300 !del.contains((SequenceI) sel.elementAt(j)))
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302 // use PID instead of Comparison (which is really not pleasant)
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303 float pid = Comparison.PID((SequenceI) sel.elementAt(j),
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304 (SequenceI) sel.elementAt(i));
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306 if (pid >= threshold)
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308 // Delete the shortest one
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309 if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel
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311 i)).getSequence().length())
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313 del.addElement(sel.elementAt(i));
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317 del.addElement(sel.elementAt(i));
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324 // Now delete the sequences
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325 for (int i = 0; i < del.size(); i++)
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327 deleteSequence((SequenceI) del.elementAt(i));
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334 public SequenceGroup findGroup(int i)
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336 return findGroup(getSequenceAt(i));
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340 public SequenceGroup findGroup(SequenceI s)
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342 for (int i = 0; i < this.groups.size(); i++)
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344 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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346 if (sg.sequences.contains(s))
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358 * @param s DOCUMENT ME!
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360 * @return DOCUMENT ME!
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362 public SequenceGroup[] findAllGroups(SequenceI s)
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364 Vector temp = new Vector();
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366 int gSize = groups.size();
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367 for (int i = 0; i < gSize; i++)
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369 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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370 if(sg==null || sg.sequences==null)
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372 this.deleteGroup(sg);
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377 if (sg.sequences.contains(s))
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379 temp.addElement(sg);
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383 SequenceGroup[] ret = new SequenceGroup[temp.size()];
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385 for (int i = 0; i < temp.size(); i++)
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387 ret[i] = (SequenceGroup) temp.elementAt(i);
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396 * @param sg DOCUMENT ME!
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398 public void addSuperGroup(SuperGroup sg)
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400 superGroup.addElement(sg);
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406 * @param sg DOCUMENT ME!
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408 public void removeSuperGroup(SuperGroup sg)
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410 superGroup.removeElement(sg);
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416 * @param sg DOCUMENT ME!
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418 * @return DOCUMENT ME!
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420 public SuperGroup getSuperGroup(SequenceGroup sg)
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422 for (int i = 0; i < this.superGroup.size(); i++)
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424 SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
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426 if (temp.sequenceGroups.contains(sg))
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436 public void addGroup(SequenceGroup sg)
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438 if (!groups.contains(sg))
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440 groups.addElement(sg);
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447 public void deleteAllGroups()
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449 groups.removeAllElements();
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450 superGroup.removeAllElements();
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454 while (i < sequences.size())
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456 SequenceI s = getSequenceAt(i);
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457 s.setColor(java.awt.Color.white);
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463 public void deleteGroup(SequenceGroup g)
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465 if (groups.contains(g))
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467 groups.removeElement(g);
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472 public SequenceI findName(String name)
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476 while (i < sequences.size())
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478 if (getSequenceAt(i).getName().equals(name))
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480 return getSequenceAt(i);
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491 public int findIndex(SequenceI s)
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495 while (i < sequences.size())
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497 if (s == getSequenceAt(i))
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511 * @return DOCUMENT ME!
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513 public int getHeight()
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515 return sequences.size();
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521 * @return DOCUMENT ME!
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523 public int getWidth()
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525 int maxLength = -1;
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527 for (int i = 0; i < sequences.size(); i++)
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529 if (getSequenceAt(i).getLength() > maxLength)
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531 maxLength = getSequenceAt(i).getLength();
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541 * @return DOCUMENT ME!
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543 public int getMaxIdLength()
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548 while (i < sequences.size())
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550 SequenceI seq = getSequenceAt(i);
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551 String tmp = seq.getName() + "/" + seq.getStart() + "-" +
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554 if (tmp.length() > max)
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556 max = tmp.length();
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568 * @param gc DOCUMENT ME!
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570 public void setGapCharacter(char gc)
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574 for (int i = 0; i < sequences.size(); i++)
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576 Sequence seq = (Sequence) sequences.elementAt(i);
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577 seq.sequence = seq.sequence.replace('.', gc);
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578 seq.sequence = seq.sequence.replace('-', gc);
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579 seq.sequence = seq.sequence.replace(' ', gc);
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586 * @return DOCUMENT ME!
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588 public char getGapCharacter()
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590 return gapCharacter;
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596 * @return DOCUMENT ME!
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598 public Vector getAAFrequency()
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600 return AAFrequency.calculate(sequences, 0, getWidth());
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606 * @return DOCUMENT ME!
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608 public boolean isAligned()
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610 int width = getWidth();
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612 for (int i = 0; i < sequences.size(); i++)
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614 if (getSequenceAt(i).getLength() != width)
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626 * @param aa DOCUMENT ME!
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628 public void deleteAnnotation(AlignmentAnnotation aa)
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632 if (annotations != null)
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634 aSize = annotations.length;
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637 AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
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641 for (int i = 0; i < aSize; i++)
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643 if (annotations[i] == aa)
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648 temp[tIndex] = annotations[i];
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652 annotations = temp;
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657 * @param aa AlignmentAnnotation
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658 * @param seqRef The sequence to associate this annotation with
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659 * @return The adjusted AlignmentAnnotation, with dataset sequence and annotation added
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661 public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef)
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665 //We can only add Annotations to the dataset sequences
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666 if(seqRef.getDatasetSequence()==null)
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671 AlignmentAnnotation [] old = seqRef.getDatasetSequence().getAnnotation();
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673 //First check if this is a new annotation or not. If it is new,
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674 //we must add the annotation to the dataset
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675 boolean newAnnotation = true;
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676 if(seqRef.getDatasetSequence().getAnnotation()!=null)
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678 for(int a=0; a<old.length; a++)
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683 newAnnotation = false;
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691 seqRef.getDatasetSequence().addAlignmentAnnotation(aa);
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694 AlignmentAnnotation copy = null;
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696 copy = new AlignmentAnnotation(
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697 aa.label, aa.description, aa.annotations, aa.graphMin,
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698 aa.graphMax, aa.graph
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701 copy = new AlignmentAnnotation(
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702 aa.label, aa.description, aa.annotations
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705 copy.datasetAnnotation = aa;
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707 addAnnotation(copy);
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709 copy.sequenceRef = seqRef;
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720 public void adjustSequenceAnnotations()
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722 if(annotations!=null)
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724 for (int a = 0; a < annotations.length; a++)
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726 if (annotations[a].sequenceRef != null)
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728 annotations[a].adjustForAlignment();
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737 * @param aa DOCUMENT ME!
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739 public void addAnnotation(AlignmentAnnotation aa)
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742 if (annotations != null)
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744 aSize = annotations.length + 1;
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747 AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
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749 temp[aSize-1] = aa;
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755 for (i = 0; i < (aSize-1); i++)
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757 temp[i] = annotations[i];
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761 annotations = temp;
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764 public void setAnnotationIndex(AlignmentAnnotation aa, int index)
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766 if(aa==null || annotations==null || annotations.length-1<index)
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769 int aSize = annotations.length;
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770 AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
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774 for (int i = 0; i < aSize; i++)
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780 temp[i] = annotations[i];
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782 temp[i] = annotations[i-1];
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785 annotations = temp;
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791 * @return DOCUMENT ME!
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793 public AlignmentAnnotation[] getAlignmentAnnotation()
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795 return annotations;
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798 public void setNucleotide(boolean b)
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806 public boolean isNucleotide()
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808 if(type==NUCLEOTIDE)
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814 public void setDataset(Alignment data)
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816 if(dataset==null && data==null)
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818 // Create a new dataset for this alignment.
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819 // Can only be done once, if dataset is not null
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820 // This will not be performed
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821 Sequence[] seqs = new Sequence[getHeight()];
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822 for (int i = 0; i < getHeight(); i++)
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825 seqs[i] = new Sequence(getSequenceAt(i).getName(),
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826 AlignSeq.extractGaps(
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827 jalview.util.Comparison.GapChars,
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828 getSequenceAt(i).getSequence()
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830 getSequenceAt(i).getStart(),
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831 getSequenceAt(i).getEnd());
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833 getSequenceAt(i).setDatasetSequence(seqs[i]);
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836 dataset = new Alignment(seqs);
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838 else if(dataset==null && data!=null)
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844 public Alignment getDataset()
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849 public boolean padGaps() {
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850 boolean modified=false;
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851 int Width = getWidth();
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853 for (int i = 0; i < sequences.size();
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856 current = getSequenceAt(i);
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858 if (current.getLength() < Width)
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860 current.insertCharAt(Width - 1, gapCharacter);
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