2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
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3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.datamodel;
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30 * Copyright: Copyright (c) 2004
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34 * Company: Dundee University
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37 * @author not attributable
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40 public class AlignmentView
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43 * Transient object compactly representing a 'view' of an alignment - with
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44 * discontinuities marked.
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46 private SeqCigar[] sequences = null;
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48 private int[] contigs = null;
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50 private int width = 0;
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52 private int firstCol = 0;
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54 public AlignmentView(CigarArray seqcigararray)
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56 if (!seqcigararray.isSeqCigarArray())
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59 "Implementation Error - can only make an alignment view from a CigarArray of sequences.");
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61 // contigs = seqcigararray.applyDeletions();
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62 contigs = seqcigararray.getDeletedRegions();
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63 sequences = seqcigararray.getSeqCigarArray();
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64 width = seqcigararray.getWidth(); // visible width
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68 * Create an alignmentView where the first column corresponds with the
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69 * 'firstcol' column of some reference alignment
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74 public AlignmentView(CigarArray sdata, int firstcol)
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77 firstCol = firstcol;
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80 public void setSequences(SeqCigar[] sequences)
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82 this.sequences = sequences;
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85 public void setContigs(int[] contigs)
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87 this.contigs = contigs;
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90 public SeqCigar[] getSequences()
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96 * @see CigarArray.getDeletedRegions
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97 * @return int[] { vis_start, sym_start, length }
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99 public int[] getContigs()
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105 * get the full alignment and a columnselection object marking the hidden
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108 * @param gapCharacter
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110 * @return Object[] { SequenceI[], ColumnSelection}
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112 public Object[] getAlignmentAndColumnSelection(char gapCharacter)
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114 ColumnSelection colsel = new ColumnSelection();
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116 return new Object[]
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118 SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
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119 contigs), colsel };
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123 * getSequenceStrings
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129 public String[] getSequenceStrings(char c)
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131 String[] seqs = new String[sequences.length];
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132 for (int n = 0; n < sequences.length; n++)
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134 String fullseq = sequences[n].getSequenceString(c);
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135 if (contigs != null)
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139 for (int h = 0; h < contigs.length; h += 3)
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141 seqs[n] += fullseq.substring(p, contigs[h + 1]);
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142 p = contigs[h + 1] + contigs[h + 2];
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144 seqs[n] += fullseq.substring(p);
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156 * @return visible number of columns in alignment view
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158 public int getWidth()
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163 protected void setWidth(int width)
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165 this.width = width;
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169 * get the contiguous subalignments in an alignment view.
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171 * @param gapCharacter
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173 * @return SequenceI[][]
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175 public SequenceI[][] getVisibleContigs(char gapCharacter)
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177 SequenceI[][] smsa;
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179 if (sequences == null || width <= 0)
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183 if (contigs != null && contigs.length > 0)
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187 int fwidth = width;
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188 for (int contig = 0; contig < contigs.length; contig += 3)
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190 if ((contigs[contig + 1] - start) > 0)
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194 fwidth += contigs[contig + 2]; // end up with full region width
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195 // (including hidden regions)
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196 start = contigs[contig + 1] + contigs[contig + 2];
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198 if (start < fwidth)
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202 smsa = new SequenceI[njobs][];
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205 for (int contig = 0; contig < contigs.length; contig += 3)
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207 if (contigs[contig + 1] - start > 0)
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209 SequenceI mseq[] = new SequenceI[sequences.length];
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210 for (int s = 0; s < mseq.length; s++)
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212 mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(
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213 start, contigs[contig + 1]);
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218 start = contigs[contig + 1] + contigs[contig + 2];
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220 if (start < fwidth)
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222 SequenceI mseq[] = new SequenceI[sequences.length];
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223 for (int s = 0; s < mseq.length; s++)
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225 mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
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234 smsa = new SequenceI[1][];
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235 smsa[0] = new SequenceI[sequences.length];
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236 for (int s = 0; s < sequences.length; s++)
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238 smsa[0][s] = sequences[s].getSeq(gapCharacter);
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245 * return full msa and hidden regions with visible blocks replaced with new
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251 * AlignmentOrder[] corresponding to each SequenceI[] block.
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254 public Object[] getUpdatedView(SequenceI[][] nvismsa,
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255 AlignmentOrder[] orders, char gapCharacter)
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257 if (sequences == null || width <= 0)
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259 throw new Error("empty view cannot be updated.");
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261 if (nvismsa == null)
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264 "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
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266 if (contigs != null && contigs.length > 0)
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268 SequenceI[] alignment = new SequenceI[sequences.length];
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269 ColumnSelection columnselection = new ColumnSelection();
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270 if (contigs != null && contigs.length > 0)
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274 int owidth = width;
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276 for (int contig = 0; contig < contigs.length; contig += 3)
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278 owidth += contigs[contig + 2]; // recover final column width
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279 if (contigs[contig + 1] - start > 0)
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281 int swidth = 0; // subalignment width
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282 if (nvismsa[j] != null)
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284 SequenceI mseq[] = nvismsa[j];
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285 AlignmentOrder order = (orders == null) ? null : orders[j];
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287 if (mseq.length != sequences.length)
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290 "Mismatch between number of sequences in block "
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291 + j + " (" + mseq.length
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292 + ") and the original view ("
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293 + sequences.length + ")");
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295 swidth = mseq[0].getLength(); // JBPNote: could ensure padded
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297 for (int s = 0; s < mseq.length; s++)
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299 if (alignment[s] == null)
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301 alignment[s] = mseq[s];
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305 alignment[s].setSequence(alignment[s]
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306 .getSequenceAsString()
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307 + mseq[s].getSequenceAsString());
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308 if (mseq[s].getStart() <= mseq[s].getEnd())
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310 alignment[s].setEnd(mseq[s].getEnd());
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314 order.updateSequence(mseq[s], alignment[s]);
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321 // recover original alignment block or place gaps
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324 // recover input data
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325 for (int s = 0; s < sequences.length; s++)
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327 SequenceI oseq = sequences[s].getSeq(gapCharacter)
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328 .getSubSequence(start, contigs[contig + 1]);
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329 if (swidth < oseq.getLength())
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331 swidth = oseq.getLength();
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333 if (alignment[s] == null)
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335 alignment[s] = oseq;
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339 alignment[s].setSequence(alignment[s]
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340 .getSequenceAsString()
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341 + oseq.getSequenceAsString());
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342 if (oseq.getEnd() >= oseq.getStart())
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344 alignment[s].setEnd(oseq.getEnd());
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354 // advance to begining of visible region
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355 start = contigs[contig + 1] + contigs[contig + 2];
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356 // add hidden segment to right of next region
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357 for (int s = 0; s < sequences.length; s++)
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359 SequenceI hseq = sequences[s].getSeq(gapCharacter)
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360 .getSubSequence(contigs[contig + 1], start);
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361 if (alignment[s] == null)
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363 alignment[s] = hseq;
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367 alignment[s].setSequence(alignment[s].getSequenceAsString()
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368 + hseq.getSequenceAsString());
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369 if (hseq.getEnd() >= hseq.getStart())
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371 alignment[s].setEnd(hseq.getEnd());
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375 // mark hidden segment as hidden in the new alignment
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376 columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2]
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378 nwidth += contigs[contig + 2];
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380 // Do final segment - if it exists
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381 if (j < nvismsa.length)
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384 if (nvismsa[j] != null)
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386 SequenceI mseq[] = nvismsa[j];
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387 AlignmentOrder order = (orders != null) ? orders[j] : null;
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388 swidth = mseq[0].getLength();
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389 for (int s = 0; s < mseq.length; s++)
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391 if (alignment[s] == null)
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393 alignment[s] = mseq[s];
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397 alignment[s].setSequence(alignment[s].getSequenceAsString()
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398 + mseq[s].getSequenceAsString());
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399 if (mseq[s].getEnd() >= mseq[s].getStart())
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401 alignment[s].setEnd(mseq[s].getEnd());
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405 order.updateSequence(mseq[s], alignment[s]);
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412 if (start < owidth)
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414 // recover input data or place gaps
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417 // recover input data
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418 for (int s = 0; s < sequences.length; s++)
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420 SequenceI oseq = sequences[s].getSeq(gapCharacter)
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421 .getSubSequence(start, owidth + 1);
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422 if (swidth < oseq.getLength())
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424 swidth = oseq.getLength();
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426 if (alignment[s] == null)
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428 alignment[s] = oseq;
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432 alignment[s].setSequence(alignment[s]
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433 .getSequenceAsString()
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434 + oseq.getSequenceAsString());
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435 if (oseq.getEnd() >= oseq.getStart())
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437 alignment[s].setEnd(oseq.getEnd());
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446 throw new Error("Padding not yet implemented.");
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452 return new Object[]
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453 { alignment, columnselection };
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457 if (nvismsa.length != 1)
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460 "Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="
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463 if (nvismsa[0] != null)
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465 return new Object[]
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466 { nvismsa[0], new ColumnSelection() };
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470 return getAlignmentAndColumnSelection(gapCharacter);
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476 * returns simple array of start end positions of visible range on alignment.
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477 * vis_start and vis_end are inclusive - use
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478 * SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence
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479 * from underlying alignment.
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481 * @return int[] { start_i, end_i } for 1<i<n visible regions.
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483 public int[] getVisibleContigs()
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485 if (contigs != null && contigs.length > 0)
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489 int fwidth = width;
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490 for (int contig = 0; contig < contigs.length; contig += 3)
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492 if ((contigs[contig + 1] - start) > 0)
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496 fwidth += contigs[contig + 2]; // end up with full region width
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497 // (including hidden regions)
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498 start = contigs[contig + 1] + contigs[contig + 2];
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500 if (start < fwidth)
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504 int viscontigs[] = new int[nvis * 2];
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507 for (int contig = 0; contig < contigs.length; contig += 3)
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509 if ((contigs[contig + 1] - start) > 0)
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511 viscontigs[nvis] = start;
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512 viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive
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515 start = contigs[contig + 1] + contigs[contig + 2];
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517 if (start < fwidth)
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519 viscontigs[nvis] = start;
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520 viscontigs[nvis + 1] = fwidth; // end is inclusive
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534 * @return position of first visible column of AlignmentView within its
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535 * parent's alignment reference frame
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537 public int getAlignmentOrigin()
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539 // TODO Auto-generated method stub
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