X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FRangetype.java;h=ee4fa8306092c72a4db5d85cd237ffdf41531d27;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=2686e858334d6e348fc1ed3ab8807f53e7b4ddce;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index 2686e85..ee4fa83 100644
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -1,35 +1,46 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
+import jalview.io.VamsasAppDatastore;
+import jalview.util.MessageManager;
+
+import java.util.List;
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;
-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()
@@ -42,6 +53,17 @@ public class Rangetype extends DatastoreItem
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
@@ -57,8 +79,8 @@ public class Rangetype extends DatastoreItem
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)
{
@@ -81,8 +103,7 @@ public class Rangetype extends DatastoreItem
// 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 };
+ se = new int[] { pos, pos };
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
@@ -116,8 +137,8 @@ public class Rangetype extends DatastoreItem
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)
{
@@ -164,8 +185,8 @@ public class Rangetype extends DatastoreItem
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)
{
@@ -205,15 +226,15 @@ public class Rangetype extends DatastoreItem
* 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 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);
}
@@ -222,12 +243,12 @@ public class Rangetype extends DatastoreItem
/**
*
* @param maprange
- * where the from range is the local mapped range, and the to
- * range is the 'mapped' range in the MapRangeType
+ * 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
+ * unit for local
* @param default
- * unit for mapped
+ * unit for mapped
* @return MapList
*/
protected jalview.util.MapList parsemapType(MapType maprange, int localu,
@@ -238,8 +259,9 @@ public class Rangetype extends DatastoreItem
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;
@@ -275,17 +297,16 @@ public class Rangetype extends DatastoreItem
* @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)
{
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());
@@ -311,6 +332,10 @@ public class Rangetype extends DatastoreItem
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))
+
}
}