{
super(alignViewport, alignPanel);
}
+ AlignmentAnnotation strucConsensus;
+ Hashtable[] hStrucConsensus;
+
public void run()
{
try
calcMan.workerComplete(this);
return;
}
- AlignmentAnnotation strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
- Hashtable[] hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
+ strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
+ hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
strucConsensus.annotations = null;
strucConsensus.annotations = new Annotation[aWidth];
// select rna struct to use for calculation
for (int i = 0; i < aa.length; i++)
{
- if (aa[i].getRNAStruc() != null)
+ if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
{
rnaStruc = aa[i];
break;
public void updateResultAnnotation(boolean immediate)
{
- AlignmentAnnotation strucConsensus = alignViewport
- .getAlignmentStrucConsensusAnnotation();
- Hashtable[] hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
if (immediate || !calcMan.isWorking(this) && strucConsensus!=null && hStrucConsensus!=null)
{
StructureFrequency.completeConsensus(strucConsensus,