/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2006 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 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 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