Title:
- * - *Description:
- * - *Copyright: Copyright (c) 2004
- * - *Company: Dundee University
- * - * @author not attributable - * @version 1.0 - */ -public class AlignmentView -{ - /** - * Transient object compactly representing a 'view' of an alignment - with discontinuities marked. - */ - private SeqCigar[] sequences = null; - private int[] contigs = null; - public AlignmentView(CigarArray seqcigararray) - { - if (!seqcigararray.isSeqCigarArray()) - throw new Error("Implementation Error - can only make an alignment view from a CigarArray of sequences."); - //contigs = seqcigararray.applyDeletions(); - contigs = seqcigararray.getDeletedRegions(); - sequences = seqcigararray.getSeqCigarArray(); - } - - public void setSequences(SeqCigar[] sequences) - { - this.sequences = sequences; - } - - public void setContigs(int[] contigs) - { - this.contigs = contigs; - } - - public SeqCigar[] getSequences() - { - return sequences; - } - - public int[] getContigs() - { - return contigs; - } - public Object[] getAlignmentAndColumnSelection(char gapCharacter) { - ColumnSelection colsel = new ColumnSelection(); - - return new Object[] { SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel, contigs), colsel}; - } - /** - * getSequenceStrings - * - * @param c char - * @return String[] - */ - public String[] getSequenceStrings(char c) - { - String[] seqs=new String[sequences.length]; - for (int n=0; n+ * Title: + *
+ * + *+ * Description: + *
+ * + *+ * Copyright: Copyright (c) 2004 + *
+ * + *+ * Company: Dundee University + *
+ * + * @author not attributable + * @version 1.0 + */ +public class AlignmentView +{ + /** + * Transient object compactly representing a 'view' of an alignment - with + * discontinuities marked. + */ + private SeqCigar[] sequences = null; + + private int[] contigs = null; + + private int width = 0; + + private int firstCol = 0; + + public AlignmentView(CigarArray seqcigararray) + { + if (!seqcigararray.isSeqCigarArray()) + { + throw new Error( + "Implementation Error - can only make an alignment view from a CigarArray of sequences."); + } + // contigs = seqcigararray.applyDeletions(); + contigs = seqcigararray.getDeletedRegions(); + sequences = seqcigararray.getSeqCigarArray(); + width = seqcigararray.getWidth(); // visible width + } + + /** + * Create an alignmentView where the first column corresponds with the + * 'firstcol' column of some reference alignment + * + * @param sdata + * @param firstcol + */ + public AlignmentView(CigarArray sdata, int firstcol) + { + this(sdata); + firstCol = firstcol; + } + + public void setSequences(SeqCigar[] sequences) + { + this.sequences = sequences; + } + + public void setContigs(int[] contigs) + { + this.contigs = contigs; + } + + public SeqCigar[] getSequences() + { + return sequences; + } + + /** + * @see CigarArray.getDeletedRegions + * @return int[] { vis_start, sym_start, length } + */ + public int[] getContigs() + { + return contigs; + } + + /** + * get the full alignment and a columnselection object marking the hidden + * regions + * + * @param gapCharacter + * char + * @return Object[] { SequenceI[], ColumnSelection} + */ + public Object[] getAlignmentAndColumnSelection(char gapCharacter) + { + ColumnSelection colsel = new ColumnSelection(); + + return new Object[] + { + SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel, + contigs), colsel }; + } + + /** + * getSequenceStrings + * + * @param c + * char + * @return String[] + */ + public String[] getSequenceStrings(char c) + { + String[] seqs = new String[sequences.length]; + for (int n = 0; n < sequences.length; n++) + { + String fullseq = sequences[n].getSequenceString(c); + if (contigs != null) + { + seqs[n] = ""; + int p = 0; + for (int h = 0; h < contigs.length; h += 3) + { + seqs[n] += fullseq.substring(p, contigs[h + 1]); + p = contigs[h + 1] + contigs[h + 2]; + } + seqs[n] += fullseq.substring(p); + } + else + { + seqs[n] = fullseq; + } + } + return seqs; + } + + /** + * + * @return visible number of columns in alignment view + */ + public int getWidth() + { + return width; + } + + protected void setWidth(int width) + { + this.width = width; + } + + /** + * get the contiguous subalignments in an alignment view. + * + * @param gapCharacter + * char + * @return SequenceI[][] + */ + public SequenceI[][] getVisibleContigs(char gapCharacter) + { + SequenceI[][] smsa; + int njobs = 1; + if (sequences == null || width <= 0) + { + return null; + } + if (contigs != null && contigs.length > 0) + { + int start = 0; + njobs = 0; + int fwidth = width; + for (int contig = 0; contig < contigs.length; contig += 3) + { + if ((contigs[contig + 1] - start) > 0) + { + njobs++; + } + fwidth += contigs[contig + 2]; // end up with full region width + // (including hidden regions) + start = contigs[contig + 1] + contigs[contig + 2]; + } + if (start < fwidth) + { + njobs++; + } + smsa = new SequenceI[njobs][]; + start = 0; + int j = 0; + for (int contig = 0; contig < contigs.length; contig += 3) + { + if (contigs[contig + 1] - start > 0) + { + SequenceI mseq[] = new SequenceI[sequences.length]; + for (int s = 0; s < mseq.length; s++) + { + mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence( + start, contigs[contig + 1]); + } + smsa[j] = mseq; + j++; + } + start = contigs[contig + 1] + contigs[contig + 2]; + } + if (start < fwidth) + { + SequenceI mseq[] = new SequenceI[sequences.length]; + for (int s = 0; s < mseq.length; s++) + { + mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start, + fwidth + 1); + } + smsa[j] = mseq; + j++; + } + } + else + { + smsa = new SequenceI[1][]; + smsa[0] = new SequenceI[sequences.length]; + for (int s = 0; s < sequences.length; s++) + { + smsa[0][s] = sequences[s].getSeq(gapCharacter); + } + } + return smsa; + } + + /** + * return full msa and hidden regions with visible blocks replaced with new + * sub alignments + * + * @param nvismsa + * SequenceI[][] + * @param orders + * AlignmentOrder[] corresponding to each SequenceI[] block. + * @return Object[] + */ + public Object[] getUpdatedView(SequenceI[][] nvismsa, + AlignmentOrder[] orders, char gapCharacter) + { + if (sequences == null || width <= 0) + { + throw new Error("empty view cannot be updated."); + } + if (nvismsa == null) + { + throw new Error( + "nvismsa==null. use getAlignmentAndColumnSelection() instead."); + } + if (contigs != null && contigs.length > 0) + { + SequenceI[] alignment = new SequenceI[sequences.length]; + ColumnSelection columnselection = new ColumnSelection(); + if (contigs != null && contigs.length > 0) + { + int start = 0; + int nwidth = 0; + int owidth = width; + int j = 0; + for (int contig = 0; contig < contigs.length; contig += 3) + { + owidth += contigs[contig + 2]; // recover final column width + if (contigs[contig + 1] - start > 0) + { + int swidth = 0; // subalignment width + if (nvismsa[j] != null) + { + SequenceI mseq[] = nvismsa[j]; + AlignmentOrder order = (orders == null) ? null : orders[j]; + j++; + if (mseq.length != sequences.length) + { + throw new Error( + "Mismatch between number of sequences in block " + + j + " (" + mseq.length + + ") and the original view (" + + sequences.length + ")"); + } + swidth = mseq[0].getLength(); // JBPNote: could ensure padded + // here. + for (int s = 0; s < mseq.length; s++) + { + if (alignment[s] == null) + { + alignment[s] = mseq[s]; + } + else + { + alignment[s].setSequence(alignment[s] + .getSequenceAsString() + + mseq[s].getSequenceAsString()); + if (mseq[s].getStart() <= mseq[s].getEnd()) + { + alignment[s].setEnd(mseq[s].getEnd()); + } + if (order != null) + { + order.updateSequence(mseq[s], alignment[s]); + } + } + } + } + else + { + // recover original alignment block or place gaps + if (true) + { + // recover input data + for (int s = 0; s < sequences.length; s++) + { + SequenceI oseq = sequences[s].getSeq(gapCharacter) + .getSubSequence(start, contigs[contig + 1]); + if (swidth < oseq.getLength()) + { + swidth = oseq.getLength(); + } + if (alignment[s] == null) + { + alignment[s] = oseq; + } + else + { + alignment[s].setSequence(alignment[s] + .getSequenceAsString() + + oseq.getSequenceAsString()); + if (oseq.getEnd() >= oseq.getStart()) + { + alignment[s].setEnd(oseq.getEnd()); + } + } + } + + } + j++; + } + nwidth += swidth; + } + // advance to begining of visible region + start = contigs[contig + 1] + contigs[contig + 2]; + // add hidden segment to right of next region + for (int s = 0; s < sequences.length; s++) + { + SequenceI hseq = sequences[s].getSeq(gapCharacter) + .getSubSequence(contigs[contig + 1], start); + if (alignment[s] == null) + { + alignment[s] = hseq; + } + else + { + alignment[s].setSequence(alignment[s].getSequenceAsString() + + hseq.getSequenceAsString()); + if (hseq.getEnd() >= hseq.getStart()) + { + alignment[s].setEnd(hseq.getEnd()); + } + } + } + // mark hidden segment as hidden in the new alignment + columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2] + - 1); + nwidth += contigs[contig + 2]; + } + // Do final segment - if it exists + if (j < nvismsa.length) + { + int swidth = 0; + if (nvismsa[j] != null) + { + SequenceI mseq[] = nvismsa[j]; + AlignmentOrder order = (orders != null) ? orders[j] : null; + swidth = mseq[0].getLength(); + for (int s = 0; s < mseq.length; s++) + { + if (alignment[s] == null) + { + alignment[s] = mseq[s]; + } + else + { + alignment[s].setSequence(alignment[s].getSequenceAsString() + + mseq[s].getSequenceAsString()); + if (mseq[s].getEnd() >= mseq[s].getStart()) + { + alignment[s].setEnd(mseq[s].getEnd()); + } + if (order != null) + { + order.updateSequence(mseq[s], alignment[s]); + } + } + } + } + else + { + if (start < owidth) + { + // recover input data or place gaps + if (true) + { + // recover input data + for (int s = 0; s < sequences.length; s++) + { + SequenceI oseq = sequences[s].getSeq(gapCharacter) + .getSubSequence(start, owidth + 1); + if (swidth < oseq.getLength()) + { + swidth = oseq.getLength(); + } + if (alignment[s] == null) + { + alignment[s] = oseq; + } + else + { + alignment[s].setSequence(alignment[s] + .getSequenceAsString() + + oseq.getSequenceAsString()); + if (oseq.getEnd() >= oseq.getStart()) + { + alignment[s].setEnd(oseq.getEnd()); + } + } + } + nwidth += swidth; + } + else + { + // place gaps. + throw new Error("Padding not yet implemented."); + } + } + } + } + } + return new Object[] + { alignment, columnselection }; + } + else + { + if (nvismsa.length != 1) + { + throw new Error( + "Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks=" + + nvismsa.length); + } + if (nvismsa[0] != null) + { + return new Object[] + { nvismsa[0], new ColumnSelection() }; + } + else + { + return getAlignmentAndColumnSelection(gapCharacter); + } + } + } + + /** + * returns simple array of start end positions of visible range on alignment. + * vis_start and vis_end are inclusive - use + * SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence + * from underlying alignment. + * + * @return int[] { start_i, end_i } for 1