/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
super(datastore);
}
- public Rangetype(VamsasAppDatastore datastore, Vobject vobj, Class jvClass)
+ public Rangetype(VamsasAppDatastore datastore, Vobject vobj,
+ Class jvClass)
{
super(datastore, vobj, jvClass);
}
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- MessageManager
- .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(MessageManager.getString(
+ "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- MessageManager
- .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(MessageManager.getString(
+ "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
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(new Integer(p));
+ posList.add(Integer.valueOf(p));
}
}
}
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
- posList.add(new Integer(pos));
+ posList.add(Integer.valueOf(pos));
}
}
}
int[] se = null;
if (range.getSegCount() > 0 && range.getPosCount() > 0)
{
- throw new Error(
- MessageManager
- .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ 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(new Integer(se[0]));
- posList.addElement(new Integer(se[1]));
+ posList.addElement(Integer.valueOf(se[0]));
+ posList.addElement(Integer.valueOf(se[1]));
}
}
else if (range.getPosCount() > 0)
for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)
{
pos = range.getPos(p).getI();
- posList.add(new Integer(pos));
- posList.add(new Integer(pos));
+ posList.add(Integer.valueOf(pos));
+ posList.add(Integer.valueOf(pos));
}
}
}
* @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
+ * @param default
+ * unit for local
+ * @param default
+ * unit for mapped
* @return MapList
*/
protected jalview.util.MapList parsemapType(MapType maprange, int localu,
int[] mappedRange = getIntervals(maprange.getMapped());
long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
: localu;
- long mu = maprange.getMapped().hasUnit() ? maprange.getMapped()
- .getUnit() : mappedu;
+ long mu = maprange.getMapped().hasUnit()
+ ? maprange.getMapped().getUnit()
+ : mappedu;
ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
(int) mu);
return ml;
if (ml == null)
{
throw new Error(
- MessageManager
- .getString("error.implementation_error_maplist_is_null"));
+ "Implementation error. MapList is null for initMapType.");
}
maprange.setLocal(new Local());
maprange.setMapped(new Mapped());