+
+ public boolean isCalcInProgress()
+ {
+ // TODO generalise to iterate over all calculators associated with av
+ return updatingConsensus || updatingConservation || updatingStrucConsensus;
+ }
+
+ public boolean isCalculationInProgress(
+ AlignmentAnnotation alignmentAnnotation)
+ {
+ if (!alignmentAnnotation.autoCalculated)
+ return false;
+ if ((updatingConsensus && consensus==alignmentAnnotation)
+ || (updatingConservation && (conservation==alignmentAnnotation || quality==alignmentAnnotation))
+ || (updatingStrucConsensus && strucConsensus==alignmentAnnotation)
+ )
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ *
+ * @return true if alignment characters should be displayed
+ */
+ public boolean isValidCharWidth()
+ {
+ return validCharWidth;
+ }
+
+ @Override
+ public Hashtable[] getSequenceConsensusHash()
+ {
+ return hconsensus;
+ }
+
+ @Override
+ public Hashtable[] getRnaStructureConsensusHash()
+ {
+ return hStrucConsensus;
+ }