package jalview.workers;
import jalview.analysis.StructureFrequency;
-import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import java.util.Hashtable;
-public class StrucConsensusThread extends AlignCalcWorker implements
- AlignCalcWorkerI
+public class StrucConsensusThread extends AlignCalcWorker
{
public StrucConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
// select rna struct to use for calculation
for (int i = 0; i < aa.length; i++)
{
- if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
+ if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
{
rnaStruc = aa[i];
break;
alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
// TODO AlignmentAnnotation rnaStruc!!!
updateResultAnnotation(true);
- if (alignViewport.getGlobalColourScheme() != null)
- {
- alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
- }
-
} catch (OutOfMemoryError error)
{
calcMan.workerCannotRun(this);
{
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
- alignViewport.getIgnoreGapsConsensus(),
+ alignViewport.isIgnoreGapsConsensus(),
alignViewport.isShowSequenceLogo(), nseq);
}
}