/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ 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.ext.rbvi.chimera;
import jalview.util.IntRangeComparator;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
/**
* A class to model a Chimera atomspec pattern, for example
*
*
* #0:15.A,28.A,54.A,63.A,70-72.A,83-84.A,97-98.A|#1:2.A,6.A,11.A,13-14.A,70.A,82.A,96-97.A
*
*
* where
*
* - #0 is a model number
* - 15 or 70-72 is a residue number, or range of residue numbers
* - .A is a chain identifier
* - residue ranges are separated by comma
* - atomspecs for distinct models are separated by | (or)
*
*
*
* @see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
*
*/
public class AtomSpecModel
{
private Map>> atomSpec;
/**
* Constructor
*/
public AtomSpecModel()
{
atomSpec = new TreeMap>>();
}
/**
* Adds one contiguous range to this atom spec
*
* @param model
* @param startPos
* @param endPos
* @param chain
*/
public void addRange(int model, int startPos, int endPos, String chain)
{
/*
* Get/initialize map of data for the colour and model
*/
Map> modelData = atomSpec.get(model);
if (modelData == null)
{
atomSpec.put(model, modelData = new TreeMap>());
}
/*
* Get/initialize map of data for colour, model and chain
*/
List chainData = modelData.get(chain);
if (chainData == null)
{
chainData = new ArrayList();
modelData.put(chain, chainData);
}
/*
* Add the start/end positions
*/
chainData.add(new int[] { startPos, endPos });
// TODO add intelligently, using a RangeList class
}
/**
* Returns the range(s) formatted as a Chimera atomspec
*
* @return
*/
public String getAtomSpec()
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
for (Integer model : atomSpec.keySet())
{
if (!firstModel)
{
sb.append("|");
}
firstModel = false;
sb.append("#").append(model).append(":");
boolean firstPositionForModel = true;
final Map> modelData = atomSpec.get(model);
for (String chain : modelData.keySet())
{
chain = chain.trim();
List rangeList = modelData.get(chain);
/*
* sort ranges into ascending start position order
*/
Collections.sort(rangeList, IntRangeComparator.ASCENDING);
int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];
Iterator iterator = rangeList.iterator();
while (iterator.hasNext())
{
int[] range = iterator.next();
if (range[0] <= end + 1)
{
/*
* range overlaps or is contiguous with the last one
* - so just extend the end position, and carry on
* (unless this is the last in the list)
*/
end = Math.max(end, range[1]);
}
else
{
/*
* we have a break so append the last range
*/
appendRange(sb, start, end, chain, firstPositionForModel);
firstPositionForModel = false;
start = range[0];
end = range[1];
}
}
/*
* and append the last range
*/
if (!rangeList.isEmpty())
{
appendRange(sb, start, end, chain, firstPositionForModel);
firstPositionForModel = false;
}
}
}
return sb.toString();
}
/**
* @param sb
* @param start
* @param end
* @param chain
* @param firstPositionForModel
*/
protected void appendRange(StringBuilder sb, int start, int end,
String chain, boolean firstPositionForModel)
{
if (!firstPositionForModel)
{
sb.append(",");
}
if (end == start)
{
sb.append(start);
}
else
{
sb.append(start).append("-").append(end);
}
if (chain.length() > 0)
{
sb.append(".").append(chain);
}
}
}