import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.api.SequenceRenderer;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
/**
* @param files
- * @param sr
* @param viewPanel
* @return
*/
@Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
+ String[] files, AlignmentViewPanel viewPanel)
{
return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, viewPanel);
+ this, viewPanel);
}
/**
continue;
}
Iterator<int[]> visible;
- if (isShowAlignmentOnly())
+ if (isShowAlignmentOnly() && isHideHiddenRegions())
{
visible = alignment.getHiddenColumns()
.getVisContigsIterator(0, width, true);