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JAL-2602 check for null or empty description when copying consensus
[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
e7f8cf2
..
96820d3
100644
(file)
--- a/
src/jalview/io/vamsas/Rangetype.java
+++ b/
src/jalview/io/vamsas/Rangetype.java
@@
-20,6
+20,10
@@
*/
package jalview.io.vamsas;
*/
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 java.util.Vector;
import uk.ac.vamsas.client.Vobject;
@@
-28,8
+32,6
@@
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.Mapped;
import uk.ac.vamsas.objects.core.RangeType;
import uk.ac.vamsas.objects.core.Seg;
-import jalview.io.VamsasAppDatastore;
-import jalview.util.MessageManager;
/**
* Enhances DatastoreItem objects with additional functions to do with RangeType
/**
* Enhances DatastoreItem objects with additional functions to do with RangeType
@@
-76,7
+78,9
@@
public abstract class Rangetype extends DatastoreItem
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
}
if (dseta.getSegCount() > 0)
{
@@
-99,8
+103,7
@@
public abstract class Rangetype extends DatastoreItem
// could do a polarity for pos range too. and pass back indication of
// discontinuities.
int pos = dseta.getPos(0).getI();
// 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();
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
@@
-134,7
+137,9
@@
public abstract class Rangetype extends DatastoreItem
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
}
if (dseta.getSegCount() > 0)
{
@@
-181,7
+186,9
@@
public abstract class Rangetype extends DatastoreItem
int[] se = null;
if (range.getSegCount() > 0 && range.getPosCount() > 0)
{
int[] se = null;
if (range.getSegCount() > 0 && range.getPosCount() > 0)
{
- throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (range.getSegCount() > 0)
{
}
if (range.getSegCount() > 0)
{
@@
-221,15
+228,15
@@
public abstract class Rangetype extends DatastoreItem
* initialise a range type object from a set of start/end inclusive intervals
*
* @param mrt
* 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();
{
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);
}
vSeg.setInclusive(true);
mrt.addSeg(vSeg);
}
@@
-297,7
+304,9
@@
public abstract class Rangetype extends DatastoreItem
{
if (ml == null)
{
{
if (ml == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_maplist_is_null"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_maplist_is_null"));
}
maprange.setLocal(new Local());
maprange.setMapped(new Mapped());
}
maprange.setLocal(new Local());
maprange.setMapped(new Mapped());