*/
package jalview.io.vamsas;
+import jalview.bin.Cache;
import jalview.io.VamsasAppDatastore;
+import jalview.util.MapList;
import jalview.util.MessageManager;
import java.util.List;
* @param default unit for mapped
* @return MapList
*/
- protected jalview.util.MapList parsemapType(MapType maprange, int localu,
+ protected MapList parsemapType(MapType maprange, int localu,
int mappedu)
{
- jalview.util.MapList ml = null;
+ 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,
+ ml = new MapList(localRange, mappedRange, (int) lu,
(int) mu);
return ml;
}
- protected jalview.util.MapList parsemapType(MapType map)
+ protected MapList parsemapType(MapType map)
{
if (!map.getLocal().hasUnit() || map.getMapped().hasUnit())
{
- jalview.bin.Cache.log
+ Cache.log
.warn("using default mapping length of 1:1 for map "
+ (map.isRegistered() ? map.getVorbaId().toString()
: ("<no Id registered> " + map.toString())));
* @param ml
* @param setUnits
*/
- protected void initMapType(MapType maprange, jalview.util.MapList ml,
+ protected void initMapType(MapType maprange, MapList ml,
boolean setUnits)
{
initMapType(maprange, ml, setUnits, false);
* @param reverse
* - reverse MapList mapping for Local and Mapped ranges and units
*/
- protected void initMapType(MapType maprange, jalview.util.MapList ml,
+ protected void initMapType(MapType maprange, MapList ml,
boolean setUnits, boolean reverse)
{
if (ml == null)