import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
StringBuffer seqs = new StringBuffer();
for (int i = 0; i < consensus.annotations.length; i++)
{
- if (consensus.annotations[i] != null)
+ Annotation annotation = consensus.annotations[i];
+ if (annotation != null)
{
- if (consensus.annotations[i].description.charAt(0) == '[')
+ String description = annotation.description;
+ if (description != null && description.startsWith("["))
{
- seqs.append(consensus.annotations[i].description.charAt(1));
+ // consensus is a tie - just pick the first one
+ seqs.append(description.charAt(1));
}
else
{
- seqs.append(consensus.annotations[i].displayCharacter);
+ seqs.append(annotation.displayCharacter);
}
}
}
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();
- complementPanel.setDontScrollComplement(true);
+ complementPanel.setToScrollComplementPanel(false);
complementPanel.scrollToCentre(sr, verticalOffset);
+ complementPanel.setToScrollComplementPanel(true);
}
}