X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FRangetype.java;h=08b1b52cea989eb33f4864469f4d7b9d3c9b70ae;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=b7e6f79d1021130ff21536192463a0d5004e9fef;hpb=cfa406a916d754e600c60f7dae29b053bf045ace;p=jalview.git
diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index b7e6f79..08b1b52 100644
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -1,18 +1,46 @@
+/*
+ * 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.
+ *
+ * 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 .
+ * 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()
@@ -25,10 +53,21 @@ 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 to vamsas utils
+ * inclusive range within which all segments and positions lie. TODO: refactor
+ * to vamsas utils
+ *
* @param dseta
* @return int[] { start, end}
*/
@@ -39,7 +78,7 @@ 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)
{
@@ -59,11 +98,11 @@ public class Rangetype extends DatastoreItem
}
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();
@@ -83,7 +122,9 @@ public class Rangetype extends DatastoreItem
}
/**
- * 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.
*/
@@ -95,7 +136,7 @@ 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)
{
@@ -112,7 +153,7 @@ public class Rangetype extends DatastoreItem
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();
@@ -125,7 +166,7 @@ public class Rangetype extends DatastoreItem
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;
@@ -135,14 +176,14 @@ public class Rangetype extends DatastoreItem
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)
{
@@ -156,7 +197,7 @@ public class Rangetype extends DatastoreItem
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();
@@ -167,28 +208,30 @@ public class Rangetype extends DatastoreItem
}
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
+ * @param ranges
*/
- protected void initRangeType(RangeType mrt, int[] range)
+ protected void initRangeType(RangeType mrt, List ranges)
{
- for (int i=0; i "+map.toString())));
+ jalview.bin.Cache.log
+ .warn("using default mapping length of 1:1 for map "
+ + (map.isRegistered() ? map.getVorbaId().toString()
+ : (" " + 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
+}