*/
package jalview.io.vamsas;
+import jalview.bin.Console;
import jalview.io.VamsasAppDatastore;
import jalview.util.MessageManager;
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));
}
}
}
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));
}
}
}
{
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()
- : ("<no Id registered> " + map.toString())));
+ Console.warn("using default mapping length of 1:1 for map "
+ + (map.isRegistered() ? map.getVorbaId().toString()
+ : ("<no Id registered> " + map.toString())));
}
return parsemapType(map, 1, 1);
}
{
if (ml == null)
{
- throw new Error(MessageManager
- .getString("error.implementation_error_maplist_is_null"));
+ throw new Error(
+ "Implementation error. MapList is null for initMapType.");
}
maprange.setLocal(new Local());
maprange.setMapped(new Mapped());