/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.datamodel; /** *

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 0) { int start = 0; int nvis = 0; int fwidth = width; for (int contig = 0; contig < contigs.length; contig += 3) { if ( (contigs[contig + 1] - start) > 0) { nvis++; } fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions) start = contigs[contig + 1] + contigs[contig + 2]; } if (start < fwidth) { nvis++; } int viscontigs[] = new int[nvis * 2]; nvis = 0; start = 0; for (int contig = 0; contig < contigs.length; contig += 3) { if ( (contigs[contig + 1] - start) > 0) { viscontigs[nvis] = start; viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive nvis += 2; } start = contigs[contig + 1] + contigs[contig + 2]; } if (start < fwidth) { viscontigs[nvis] = start; viscontigs[nvis + 1] = fwidth; // end is inclusive nvis += 2; } return viscontigs; } else { return new int[] { 0, width}; } } /** * * @return position of first visible column of AlignmentView within its parent's alignment reference frame */ public int getAlignmentOrigin() { // TODO Auto-generated method stub return firstCol; } }