/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview 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 3
* of the License, or (at your option) any later version.
*
* Jalview 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 Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
import java.util.ArrayList;
import java.util.List;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentI;
/**
* grab bag of useful alignment manipulation operations Expect these to be
* refactored elsewhere at some point.
*
* @author jimp
*
*/
public class AlignmentUtils
{
/**
* given an existing alignment, create a new alignment including all, or up to
* flankSize additional symbols from each sequence's dataset sequence
*
* @param core
* @param flankSize
* @return AlignmentI
*/
public static AlignmentI expandContext(AlignmentI core, int flankSize)
{
List sq = new ArrayList();
int maxoffset = 0;
for (SequenceI s : core.getSequences())
{
SequenceI newSeq = s.deriveSequence();
if (newSeq.getStart() > maxoffset
&& newSeq.getDatasetSequence().getStart() < s.getStart())
{
maxoffset = newSeq.getStart();
}
sq.add(newSeq);
}
if (flankSize > -1)
{
maxoffset = flankSize;
}
// now add offset to create a new expanded alignment
for (SequenceI s : sq)
{
SequenceI ds = s;
while (ds.getDatasetSequence() != null)
{
ds = ds.getDatasetSequence();
}
int s_end = s.findPosition(s.getStart() + s.getLength());
// find available flanking residues for sequence
int ustream_ds = s.getStart() - ds.getStart(), dstream_ds = ds
.getEnd() - s_end;
// build new flanked sequence
// compute gap padding to start of flanking sequence
int offset = maxoffset - ustream_ds;
// padding is gapChar x ( maxoffset - min(ustream_ds, flank)
if (flankSize >= 0)
{
if (flankSize < ustream_ds)
{
// take up to flankSize residues
offset = maxoffset - flankSize;
ustream_ds = flankSize;
}
if (flankSize < dstream_ds)
{
dstream_ds = flankSize;
}
}
char[] upstream = new String(ds.getSequence(s.getStart() - 1
- ustream_ds, s.getStart() - 1)).toLowerCase().toCharArray();
char[] downstream = new String(ds.getSequence(s_end - 1, s_end + 1
+ dstream_ds)).toLowerCase().toCharArray();
char[] coreseq = s.getSequence();
char[] nseq = new char[offset + upstream.length + downstream.length
+ coreseq.length];
char c = core.getGapCharacter();
// TODO could lowercase the flanking regions
int p = 0;
for (; p < offset; p++)
{
nseq[p] = c;
}
// s.setSequence(new String(upstream).toLowerCase()+new String(coreseq) +
// new String(downstream).toLowerCase());
System.arraycopy(upstream, 0, nseq, p, upstream.length);
System.arraycopy(coreseq, 0, nseq, p + upstream.length,
coreseq.length);
System.arraycopy(downstream, 0, nseq, p + coreseq.length
+ upstream.length, downstream.length);
s.setSequence(new String(nseq));
s.setStart(s.getStart() - ustream_ds);
s.setEnd(s_end + downstream.length);
}
AlignmentI newAl = new jalview.datamodel.Alignment(
sq.toArray(new SequenceI[0]));
newAl.setDataset(core.getDataset());
return newAl;
}
}