import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
+import jalview.renderer.ResidueShaderI;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.schemabinding.version2.Annotation;
import jalview.schemabinding.version2.UserColours;
import jalview.schemabinding.version2.Viewport;
import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.CollectionColourSchemeI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.FeatureColour;
ColourSchemeI colourScheme = sg.getColourScheme();
if (colourScheme != null)
{
- CollectionColourSchemeI groupColourScheme = sg
+ ResidueShaderI groupColourScheme = sg
.getGroupColourScheme();
if (groupColourScheme.conservationApplied())
{
.getGlobalColourScheme()));
}
- CollectionColourSchemeI vcs = av.getViewportColourScheme();
+ ResidueShaderI vcs = av.getResidueShading();
ColourSchemeI cs = av.getGlobalColourScheme();
if (cs != null)
jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
sg.getGroupColourScheme().setThreshold(pidThreshold, true);
+ sg.getGroupColourScheme().setConservationInc(jGroup.getConsThreshold());
sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
sg.textColour = new java.awt.Color(jGroup.getTextCol1());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
+ af.viewport.setThreshold(view.getPidThreshold());
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
+ af.viewport.setIncrement(view.getConsThreshold());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setRightAlignIds(view.getRightAlignIds());
af.viewport.setFont(
{
cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
}
-
- // if (cs != null)
- // {
- // cs.setThreshold(view.getPidThreshold(), true);
- // cs.setConsensus(af.viewport.getSequenceConsensusHash());
- // }
}
af.viewport.setGlobalColourScheme(cs);
- af.viewport.getViewportColourScheme().setThreshold(
+ af.viewport.getResidueShading().setThreshold(
view.getPidThreshold(), true);
- af.viewport.getViewportColourScheme().setConsensus(
+ af.viewport.getResidueShading().setConsensus(
af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
if (view.getConservationSelected() && cs != null)
{
- af.viewport.getViewportColourScheme().setConservationInc(
+ af.viewport.getResidueShading().setConservationInc(
view.getConsThreshold());
}