import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
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;
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();
hconsensus = av.getSequenceConsensusHash();