public void adjustForAlignment()
{
- if (sequenceRef == null || sequenceMapping == null
- || annotations == null)
+ if (sequenceRef == null)
+ {
+ return;
+ }
+
+ if (annotations == null)
{
return;
}
for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
{
index = new Integer(a);
- if (sequenceMapping.containsKey(index))
+ if (sequenceMapping != null && sequenceMapping.containsKey(index))
{
position = sequenceRef.findIndex(a) - 1;