git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
patch for occasional ArrayIndexOutOfBounds
[jalview.git]
/
src
/
jalview
/
io
/
vamsas
/
Rangetype.java
diff --git
a/src/jalview/io/vamsas/Rangetype.java
b/src/jalview/io/vamsas/Rangetype.java
index
2686e85
..
c4b817d
100644
(file)
--- a/
src/jalview/io/vamsas/Rangetype.java
+++ b/
src/jalview/io/vamsas/Rangetype.java
@@
-1,35
+1,43
@@
/*
/*
- * 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 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
*
- * 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.
*
*
- * 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
+ * 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/>.
*/
package jalview.io.vamsas;
import java.util.Vector;
*/
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 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.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.io.VamsasAppDatastore;
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()
{
public Rangetype()
@@
-42,6
+50,16
@@
public class Rangetype extends DatastoreItem
super(datastore);
}
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
/**
* get real bounds of a RangeType's specification. start and end are an
* inclusive range within which all segments and positions lie. TODO: refactor
@@
-222,12
+240,10
@@
public class Rangetype extends DatastoreItem
/**
*
* @param maprange
/**
*
* @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
+ * 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,
* @return MapList
*/
protected jalview.util.MapList parsemapType(MapType maprange, int localu,
@@
-275,9
+291,8
@@
public class Rangetype extends DatastoreItem
* @param maprange
* @param ml
* @param setUnits
* @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)
@@
-311,6
+326,10
@@
public class Rangetype extends DatastoreItem
maprange.getLocal().setUnit(ml.getToRatio());
maprange.getMapped().setUnit(ml.getFromRatio());
}
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))
+
}
}
}
}