import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.ProfilesI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.NucleotideColourScheme;
ResidueShaderI profcolour = null;
private ColumnSelection columnSelection;
+
+ private HiddenColumns hiddenColumns;
private ProfilesI hconsensus;
profcolour = new ResidueShader(col);
}
columnSelection = av.getColumnSelection();
+ hiddenColumns = av.getAlignment().getHiddenColumns();
hconsensus = av.getSequenceConsensusHash();
complementConsensus = av.getComplementConsensusHash();
hStrucConsensus = av.getRnaStructureConsensusHash();
{
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(startRes + x);
+ column = hiddenColumns.adjustForHiddenColumns(startRes + x);
if (column > row_annotations.length - 1)
{
break;
column = sRes + x;
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(column);
+ column = hiddenColumns.adjustForHiddenColumns(column);
}
if (column > aaMax)
column = sRes + x;
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(column);
+ column = hiddenColumns.adjustForHiddenColumns(column);
}
if (column > aaMax)