import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
-import jalview.gui.FeatureRenderer;
import jalview.gui.JvOptionPane;
import jalview.gui.PCAPanel;
import jalview.gui.PopupMenu;
import jalview.structure.StructureImportSettings;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import java.awt.Color;
import java.io.File;
DataSourceType.FILE);
assertNotNull(af, "Didn't read input file " + inFile);
af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
- assertSame(af.getViewport().getGlobalColourScheme().getClass(),
+ AlignViewport viewport = af.getViewport();
+ assertSame(viewport.getGlobalColourScheme().getClass(),
TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
assertNotNull(
- ColourSchemeProperty.getColourScheme(
- af.getViewport().getAlignment(),
- af.getViewport().getGlobalColourScheme()
+ ColourSchemeProperty.getColourScheme(viewport,
+ viewport.getAlignment(),
+ viewport.getGlobalColourScheme()
.getSchemeName()),
"Recognise T-Coffee score from string");
/*
* Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
*/
+ av.setColourAppliesToAllGroups(false);
af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
af.abovePIDThreshold_actionPerformed(true);
/*
* set colour schemes for features
*/
- FeatureRenderer fr = af.getFeatureRenderer();
+ FeatureRendererModel fr = af.getFeatureRenderer();
fr.findAllFeatures(true);
// type1: red
fr.setColour("type2", byLabel);
// type3: by score above threshold
- FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
- 10);
+ FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byScore.setAboveThreshold(true);
byScore.setThreshold(2f);
fr.setColour("type3", byScore);
fr.setColour("type4", byAF);
// type5: by attribute CSQ:PolyPhen below threshold
- FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
- 1, 10);
+ FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byPolyPhen.setBelowThreshold(true);
byPolyPhen.setThreshold(3f);
byPolyPhen.setAttributeName("CSQ", "PolyPhen");