/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
* 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
+import jalview.bin.Cache;
+import jalview.io.VamsasAppDatastore;
+import jalview.util.MapList;
+import jalview.util.MessageManager;
+
+import java.util.List;
import java.util.Vector;
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.Mapped;
import uk.ac.vamsas.objects.core.RangeType;
import uk.ac.vamsas.objects.core.Seg;
-import jalview.io.VamsasAppDatastore;
/**
* Enhances DatastoreItem objects with additional functions to do with RangeType
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ 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(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
int[] se = null;
if (range.getSegCount() > 0 && range.getPosCount() > 0)
{
- throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (range.getSegCount() > 0)
{
* initialise a range type object from a set of start/end inclusive intervals
*
* @param mrt
- * @param range
+ * @param ranges
*/
- protected void initRangeType(RangeType mrt, int[] range)
+ protected void initRangeType(RangeType mrt, List<int[]> ranges)
{
- for (int i = 0; i < range.length; i += 2)
+ for (int[] range : ranges)
{
Seg vSeg = new Seg();
- vSeg.setStart(range[i]);
- vSeg.setEnd(range[i + 1]);
+ vSeg.setStart(range[0]);
+ vSeg.setEnd(range[1]);
vSeg.setInclusive(true);
mrt.addSeg(vSeg);
}
* @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)
{
- throw new Error(
- "Implementation error. MapList is null for initMapType.");
+ throw new Error(MessageManager.getString("error.implementation_error_maplist_is_null"));
}
maprange.setLocal(new Local());
maprange.setMapped(new Mapped());