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JAL-2738 error logging if no ##reference found
[jalview.git]
/
test
/
jalview
/
project
/
Jalview2xmlTests.java
diff --git
a/test/jalview/project/Jalview2xmlTests.java
b/test/jalview/project/Jalview2xmlTests.java
index
d6df39a
..
d902fa2
100644
(file)
--- a/
test/jalview/project/Jalview2xmlTests.java
+++ b/
test/jalview/project/Jalview2xmlTests.java
@@
-147,12
+147,13
@@
public class Jalview2xmlTests extends Jalview2xmlBase
DataSourceType.FILE);
assertNotNull(af, "Didn't read input file " + inFile);
af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
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(
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");
.getSchemeName()),
"Recognise T-Coffee score from string");
@@
-818,6
+819,7
@@
public class Jalview2xmlTests extends Jalview2xmlBase
/*
* Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
*/
/*
* 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);
af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
af.abovePIDThreshold_actionPerformed(true);
@@
-930,8
+932,8
@@
public class Jalview2xmlTests extends Jalview2xmlBase
fr.setColour("type2", byLabel);
// type3: by score above threshold
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);
byScore.setAboveThreshold(true);
byScore.setThreshold(2f);
fr.setColour("type3", byScore);
@@
-943,8
+945,8
@@
public class Jalview2xmlTests extends Jalview2xmlBase
fr.setColour("type4", byAF);
// type5: by attribute CSQ:PolyPhen below threshold
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");
byPolyPhen.setBelowThreshold(true);
byPolyPhen.setThreshold(3f);
byPolyPhen.setAttributeName("CSQ", "PolyPhen");