/*******************************************************************************
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* 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 .
*******************************************************************************/
package jalview.ws.rest.params;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.IntegerParameter;
import jalview.ws.params.simple.Option;
import jalview.ws.rest.AlignmentProcessor;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import jalview.ws.rest.RestJob;
import jalview.ws.rest.RestServiceDescription;
import jalview.ws.rest.InputType.molType;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Vector;
import org.apache.http.entity.mime.content.ContentBody;
import org.apache.http.entity.mime.content.StringBody;
/**
* Represents the partitions defined on the alignment as indices e.g. for a
* partition (A,B,C),(D,E),(F) The indices would be 3,2,1. Note, the alignment
* must be ordered so groups are contiguous before this input type can be used.
*
* @author JimP
*
*/
public class SeqGroupIndexVector extends InputType implements
AlignmentProcessor
{
public SeqGroupIndexVector()
{
super(new Class[]
{ AlignmentI.class });
}
/**
* separator for list of sequence Indices - default is ','
*/
public String sep = ",";
/**
* min size of each partition
*/
public int minsize = 1;
molType type;
/**
* prepare the context alignment for this input
*
* @param al
* - alignment to be processed
* @return al or a new alignment with appropriate attributes/order for input
*/
public AlignmentI prepareAlignment(AlignmentI al)
{
jalview.analysis.AlignmentSorter.sortByGroup(al);
return al;
}
@Override
public ContentBody formatForInput(RestJob rj)
throws UnsupportedEncodingException, NoValidInputDataException
{
StringBuffer idvector = new StringBuffer();
boolean list = false;
AlignmentI al = rj.getAlignmentForInput(token, type);
// assume that alignment is properly ordered so groups form consecutive
// blocks
ArrayList gl = new ArrayList();
int p = 0;
for (SequenceGroup sg : (Vector) al.getGroups())
{
if (sg.getSize() < minsize)
{
throw new NoValidInputDataException("Group contains less than "
+ minsize + " sequences.");
}
// TODO: refactor to sequenceGroup for efficiency -
// getAlignmentRowInterval(AlignmentI al)
int[] se = null;
for (SequenceI sq : sg.getSequencesInOrder(al))
{
p = al.findIndex(sq);
if (se == null)
{
se = new int[]
{ p, p };
}
else
{
if (p < se[0])
se[0] = p;
if (p > se[1])
se[1] = p;
}
}
if (se != null)
{
gl.add(se);
}
}
// are there any more sequences ungrouped that should be added as a single
// remaining group ? - these might be at the start or the end
if (gl.size() > 0)
{
int[] tail = gl.get(0);
if (tail[0] > 0)
{
if (1 + tail[0] > minsize)
{
gl.add(0, new int[]
{ 0, tail[0] - 1 });
}
else
{
// lets be intelligent here - if the remaining sequences aren't enough
// to make a final group, then don't make one.
// throw new
// NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
}
}
else
{
tail = gl.get(gl.size() - 1);
if (1 + tail[1] < al.getHeight())
{
if (al.getHeight() - (1 + tail[1]) > minsize)
{
gl.add(new int[]
{ tail[1] + 1, al.getHeight() - 1 });
}
else
{
// lets be intelligent here - if the remaining sequences aren't
// enough to make a final group, then don't make one.
// throw new
// NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
}
}
}
}
else
{
gl.add(new int[]
{ 0, al.getHeight() - 1 });
}
if (min >= 0 && gl.size() < min)
{
throw new NoValidInputDataException(
"Not enough sequence groups for input. Need at least " + min
+ " groups (including ungrouped regions).");
}
if (max > 0 && gl.size() > max)
{
throw new NoValidInputDataException(
"Too many sequence groups for input. Need at most " + max
+ " groups (including ungrouped regions).");
}
int[][] vals = gl.toArray(new int[gl.size()][]);
int[] srt = new int[gl.size()];
for (int i = 0; i < vals.length; i++)
srt[i] = vals[i][0];
jalview.util.QuickSort.sort(srt, vals);
list = false;
int last = vals[0][0] - 1;
for (int[] range : vals)
{
if (range[1] > last)
{
if (list)
{
idvector.append(sep);
}
idvector.append(range[1] - last);
last = range[1];
list = true;
}
}
return new StringBody(idvector.toString());
}
/**
* set minimum number of sequences allowed in a partition. Default is 1
* sequence.
*
* @param i
* (number greater than 1)
*/
public void setMinsize(int i)
{
if (minsize >= 1)
{
minsize = i;
}
else
{
minsize = 1;
}
}
@Override
public List getURLEncodedParameter()
{
ArrayList prms = new ArrayList();
super.addBaseParams(prms);
prms.add("minsize='" + minsize + "'");
prms.add("sep='" + sep + "'");
if (type != null)
{
prms.add("type='" + type + "'");
}
return prms;
}
@Override
public String getURLtokenPrefix()
{
return "PARTITION";
}
@Override
public boolean configureProperty(String tok, String val,
StringBuffer warnings)
{
if (tok.startsWith("sep"))
{
sep = val;
return true;
}
if (tok.startsWith("minsize"))
{
try
{
minsize = Integer.valueOf(val);
if (minsize >= 0)
return true;
} catch (Exception x)
{
}
warnings.append("Invalid minsize value '" + val
+ "'. Must be a positive integer.\n");
}
if (tok.startsWith("type"))
{
try
{
type = molType.valueOf(val);
return true;
} catch (Exception x)
{
warnings.append("Invalid molecule type '" + val
+ "'. Must be one of (");
for (molType v : molType.values())
{
warnings.append(" " + v);
}
warnings.append(")\n");
}
}
return false;
}
@Override
public List getOptions()
{
List lst = getBaseOptions();
lst.add(new Option("sep",
"Separator character between elements of vector", true, ",",
sep, Arrays.asList(new String[]
{ " ", ",", ";", "\t", "|" }), null));
lst.add(new IntegerParameter("minsize", "Minimum size of partition allowed by service", true, 1, minsize, 1,0));
lst.add(createMolTypeOption("type", "Sequence type", false, type, molType.MIX));
return lst;
}
}