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JAl-1705 ENSEMBL cDNA type cannot be queried with peptide IDs
[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
a2b5ff4
..
08b1b52
100644
(file)
--- a/
src/jalview/io/vamsas/Rangetype.java
+++ b/
src/jalview/io/vamsas/Rangetype.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-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;
@@
-28,7
+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;
/**
* Enhances DatastoreItem objects with additional functions to do with RangeType
/**
* Enhances DatastoreItem objects with additional functions to do with RangeType
@@
-75,8
+78,7
@@
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(
- "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.getSegCount() > 0)
{
@@
-134,8
+136,7
@@
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(
- "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.getSegCount() > 0)
{
@@
-182,8
+183,7
@@
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(
- "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)
{
}
if (range.getSegCount() > 0)
{
@@
-223,15
+223,15
@@
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);
}
@@
-299,8
+299,7
@@
public abstract class Rangetype extends DatastoreItem
{
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());
}
maprange.setLocal(new Local());
maprange.setMapped(new Mapped());