+/*
+ * 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;
/**
*/
public class AlignmentView
{
- /**
- * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
- */
- private SeqCigar[] sequences = null;
+ /**
+ * 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 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;
return sequences;
}
+ /**
+ * @see CigarArray.getDeletedRegions
+ * @return int[] { vis_start, sym_start, length }
+ */
public int[] getContigs()
{
return contigs;
}
- public Object[] getAlignmentAndColumnSelection(char gapCharacter) {
+
+ /**
+ * 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};
+ return new Object[]
+ {
+ SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
+ contigs), colsel};
}
+
/**
* getSequenceStrings
*
*/
public String[] getSequenceStrings(char c)
{
- String[] seqs=new String[sequences.length];
- for (int n=0; n<sequences.length; n++) {
- seqs[n] = sequences[n].getSequenceString(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() {
+ public int getWidth()
+ {
return width;
}
- protected void setWidth(int 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<i<n visible regions.
+ */
+ public int[] getVisibleContigs()
+ {
+ if (contigs != null && contigs.length > 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff