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JAL-1668 further clean-up of popup menu and NPE check while transfering ResNum featur...
[jalview.git]
/
src
/
jalview
/
gui
/
Jalview2XML.java
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
3f3e8f6
..
2799a7e
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-163,7
+163,7
@@
public class Jalview2XML
*/
Map<String, SequenceI> seqRefIds = null;
*/
Map<String, SequenceI> seqRefIds = null;
- Vector frefedSequence = null;
+ Vector<Object[]> frefedSequence = null;
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
@@
-258,7
+258,7
@@
public class Jalview2XML
int r = 0, rSize = frefedSequence.size();
while (r < rSize)
{
int r = 0, rSize = frefedSequence.size();
while (r < rSize)
{
- Object[] ref = (Object[]) frefedSequence.elementAt(r);
+ Object[] ref = frefedSequence.elementAt(r);
if (ref != null)
{
String sref = (String) ref[0];
if (ref != null)
{
String sref = (String) ref[0];
@@
-2254,7
+2254,7
@@
public class Jalview2XML
}
if (frefedSequence == null)
{
}
if (frefedSequence == null)
{
- frefedSequence = new Vector();
+ frefedSequence = new Vector<Object[]>();
}
AlignFrame af = null, _af = null;
}
AlignFrame af = null, _af = null;
@@
-2850,7
+2850,7
@@
public class Jalview2XML
{
mapping = addMapping(maps[m].getMapping());
}
{
mapping = addMapping(maps[m].getMapping());
}
- if (dnaseq != null)
+ if (dnaseq != null && mapping.getTo() != null)
{
cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
}
{
cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
}