import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.ProfilesI;
-import jalview.schemes.CollectionColourScheme;
-import jalview.schemes.CollectionColourSchemeI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.ResidueProperties;
boolean av_renderHistogram = true, av_renderProfile = true,
av_normaliseProfile = false;
- CollectionColourSchemeI profcolour = null;
+ ResidueShaderI profcolour = null;
private ColumnSelection columnSelection;
+
+ private HiddenColumns hiddenColumns;
private ProfilesI hconsensus;
public void updateFromAlignViewport(AlignViewportI av)
{
charWidth = av.getCharWidth();
- endRes = av.getEndRes();
+ endRes = av.getRanges().getEndRes();
charHeight = av.getCharHeight();
hasHiddenColumns = av.hasHiddenColumns();
validCharWidth = av.isValidCharWidth();
av_renderHistogram = av.isShowConsensusHistogram();
av_renderProfile = av.isShowSequenceLogo();
av_normaliseProfile = av.isNormaliseSequenceLogo();
- profcolour = av.getViewportColourScheme();
+ profcolour = av.getResidueShading();
if (profcolour == null || profcolour.getColourScheme() == null)
{
/*
*/
ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme()
: new ZappoColourScheme();
- profcolour = new CollectionColourScheme(col);
+ 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)