/*
* 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.io.vamsas;
import jalview.io.VamsasAppDatastore;
import jalview.util.MessageManager;
import java.util.List;
import java.util.Vector;
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.Local;
import uk.ac.vamsas.objects.core.MapType;
import uk.ac.vamsas.objects.core.Mapped;
import uk.ac.vamsas.objects.core.RangeType;
import uk.ac.vamsas.objects.core.Seg;
/**
* Enhances DatastoreItem objects with additional functions to do with RangeType
* objects
*
* @author JimP
*
*/
public abstract class Rangetype extends DatastoreItem
{
public Rangetype()
{
super();
}
public Rangetype(VamsasAppDatastore datastore)
{
super(datastore);
}
public Rangetype(VamsasAppDatastore datastore, Vobject vobj,
Class jvClass)
{
super(datastore, vobj, jvClass);
}
public Rangetype(VamsasAppDatastore datastore, Object jvobj, Class vClass)
{
super(datastore, jvobj, vClass);
}
/**
* get real bounds of a RangeType's specification. start and end are an
* inclusive range within which all segments and positions lie. TODO: refactor
* to vamsas utils
*
* @param dseta
* @return int[] { start, end}
*/
protected int[] getBounds(RangeType dseta)
{
if (dseta != null)
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
throw new Error(MessageManager.getString(
"error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
se = getSegRange(dseta.getSeg(0), true);
for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
{
int nse[] = getSegRange(dseta.getSeg(s), true);
if (se[0] > nse[0])
{
se[0] = nse[0];
}
if (se[1] < nse[1])
{
se[1] = nse[1];
}
}
}
if (dseta.getPosCount() > 0)
{
// could do a polarity for pos range too. and pass back indication of
// discontinuities.
int pos = dseta.getPos(0).getI();
se = new int[] { pos, pos };
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
if (se[0] > pos)
{
se[0] = pos;
}
if (se[1] < pos)
{
se[1] = pos;
}
}
}
return se;
}
return null;
}
/**
* map from a rangeType's internal frame to the referenced object's coordinate
* frame.
*
* @param dseta
* @return int [] { ref(pos)...} for all pos in rangeType's frame.
*/
protected int[] getMapping(RangeType dseta)
{
Vector posList = new Vector();
if (dseta != null)
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
throw new Error(MessageManager.getString(
"error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
{
se = getSegRange(dseta.getSeg(s), false);
int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
{
posList.add(Integer.valueOf(p));
}
}
}
else if (dseta.getPosCount() > 0)
{
int pos = dseta.getPos(0).getI();
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
posList.add(Integer.valueOf(pos));
}
}
}
if (posList != null && posList.size() > 0)
{
int[] range = new int[posList.size()];
for (int i = 0; i < range.length; i++)
{
range[i] = ((Integer) posList.elementAt(i)).intValue();
}
posList.clear();
return range;
}
return null;
}
protected int[] getIntervals(RangeType range)
{
int[] intervals = null;
Vector posList = new Vector();
if (range != null)
{
int[] se = null;
if (range.getSegCount() > 0 && range.getPosCount() > 0)
{
throw new Error(MessageManager.getString(
"error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (range.getSegCount() > 0)
{
for (int s = 0, sSize = range.getSegCount(); s < sSize; s++)
{
se = getSegRange(range.getSeg(s), false);
posList.addElement(Integer.valueOf(se[0]));
posList.addElement(Integer.valueOf(se[1]));
}
}
else if (range.getPosCount() > 0)
{
int pos = range.getPos(0).getI();
for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)
{
pos = range.getPos(p).getI();
posList.add(Integer.valueOf(pos));
posList.add(Integer.valueOf(pos));
}
}
}
if (posList != null && posList.size() > 0)
{
intervals = new int[posList.size()];
java.util.Enumeration e = posList.elements();
int i = 0;
while (e.hasMoreElements())
{
intervals[i++] = ((Integer) e.nextElement()).intValue();
}
}
return intervals;
}
/**
* initialise a range type object from a set of start/end inclusive intervals
*
* @param mrt
* @param ranges
*/
protected void initRangeType(RangeType mrt, List ranges)
{
for (int[] range : ranges)
{
Seg vSeg = new Seg();
vSeg.setStart(range[0]);
vSeg.setEnd(range[1]);
vSeg.setInclusive(true);
mrt.addSeg(vSeg);
}
}
/**
*
* @param maprange
* where the from range is the local mapped range, and the to range
* is the 'mapped' range in the MapRangeType
* @param default
* unit for local
* @param default
* unit for mapped
* @return MapList
*/
protected jalview.util.MapList parsemapType(MapType maprange, int localu,
int mappedu)
{
jalview.util.MapList ml = null;
int[] localRange = getIntervals(maprange.getLocal());
int[] mappedRange = getIntervals(maprange.getMapped());
long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
: localu;
long mu = maprange.getMapped().hasUnit()
? maprange.getMapped().getUnit()
: mappedu;
ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
(int) mu);
return ml;
}
protected jalview.util.MapList parsemapType(MapType map)
{
if (!map.getLocal().hasUnit() || map.getMapped().hasUnit())
{
jalview.bin.Cache.log
.warn("using default mapping length of 1:1 for map "
+ (map.isRegistered() ? map.getVorbaId().toString()
: (" " + map.toString())));
}
return parsemapType(map, 1, 1);
}
/**
* initialise a MapType object from a MapList object.
*
* @param maprange
* @param ml
* @param setUnits
*/
protected void initMapType(MapType maprange, jalview.util.MapList ml,
boolean setUnits)
{
initMapType(maprange, ml, setUnits, false);
}
/**
*
* @param maprange
* @param ml
* @param setUnits
* @param reverse
* - reverse MapList mapping for Local and Mapped ranges and units
*/
protected void initMapType(MapType maprange, jalview.util.MapList ml,
boolean setUnits, boolean reverse)
{
if (ml == null)
{
throw new Error(MessageManager
.getString("error.implementation_error_maplist_is_null"));
}
maprange.setLocal(new Local());
maprange.setMapped(new Mapped());
if (!reverse)
{
initRangeType(maprange.getLocal(), ml.getFromRanges());
initRangeType(maprange.getMapped(), ml.getToRanges());
}
else
{
initRangeType(maprange.getLocal(), ml.getToRanges());
initRangeType(maprange.getMapped(), ml.getFromRanges());
}
if (setUnits)
{
if (!reverse)
{
maprange.getLocal().setUnit(ml.getFromRatio());
maprange.getMapped().setUnit(ml.getToRatio());
}
else
{
maprange.getLocal().setUnit(ml.getToRatio());
maprange.getMapped().setUnit(ml.getFromRatio());
}
// TODO: and verify - raise an implementation fault notice if local/mapped
// range % Local/Mapped Ratio != 0
// if (uk.ac.vamsas.objects.utils.Range.getIntervals(range))
}
}
}