+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io.vamsas;
-
import java.util.Vector;
+import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.Local;
-import uk.ac.vamsas.objects.core.Map;
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;
-import jalview.datamodel.Mapping;
import jalview.io.VamsasAppDatastore;
+import jalview.util.MessageManager;
-public class Rangetype extends DatastoreItem
+/**
+ * Enhances DatastoreItem objects with additional functions to do with RangeType
+ * objects
+ *
+ * @author JimP
+ *
+ */
+public abstract class Rangetype extends DatastoreItem
{
public Rangetype()
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
+ * inclusive range within which all segments and positions lie. TODO: refactor
+ * to vamsas utils
+ *
* @param dseta
* @return int[] { start, end}
*/
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)
{
}
if (dseta.getPosCount() > 0)
{
- // could do a polarity for pos range too. and pass back indication of discontinuities.
+ // 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};
+ { pos, pos };
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
}
/**
- * map from a rangeType's internal frame to the referenced object's coordinate frame.
+ * 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.
*/
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)
{
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();
int[] range = new int[posList.size()];
for (int i = 0; i < range.length; i++)
{
- range[i] = ( (Integer) posList.elementAt(i)).intValue();
+ range[i] = ((Integer) posList.elementAt(i)).intValue();
}
posList.clear();
return range;
protected int[] getIntervals(RangeType range)
{
- int[] intervals=null;
+ int[] intervals = null;
Vector posList = new Vector();
if (range != null)
{
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)
{
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();
}
if (posList != null && posList.size() > 0)
{
- intervals=new int[posList.size()];
+ intervals = new int[posList.size()];
java.util.Enumeration e = posList.elements();
- int i=0;
+ int i = 0;
while (e.hasMoreElements())
{
- intervals[i++] = ((Integer)e.nextElement()).intValue();
+ intervals[i++] = ((Integer) e.nextElement()).intValue();
}
}
return intervals;
}
+
/**
* initialise a range type object from a set of start/end inclusive intervals
+ *
* @param mrt
* @param range
*/
protected void initRangeType(RangeType mrt, int[] range)
{
- for (int i=0; i<range.length; i+=2)
+ for (int i = 0; i < range.length; i += 2)
{
Seg vSeg = new Seg();
vSeg.setStart(range[i]);
- vSeg.setEnd(range[i+1]);
+ vSeg.setEnd(range[i + 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 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)
+ 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);
+ 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() : ("<no Id registered> "+map.toString())));
+ jalview.bin.Cache.log
+ .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);
+ 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)
+ 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
+ * @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)
+ protected void initMapType(MapType maprange, jalview.util.MapList ml,
+ boolean setUnits, boolean reverse)
{
- if (ml==null)
+ 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());
if (!reverse)
- {
+ {
initRangeType(maprange.getLocal(), ml.getFromRanges());
initRangeType(maprange.getMapped(), ml.getToRanges());
- } else {
- initRangeType(maprange.getLocal(), ml.getToRanges());
- initRangeType(maprange.getMapped(), ml.getFromRanges());
- }
+ }
+ 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 {
+ }
+ 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))
+
}
}
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / blobdiff