git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...
[jalview.git]
/
test
/
jalview
/
io
/
Jalview2xmlTests.java
diff --git
a/test/jalview/io/Jalview2xmlTests.java
b/test/jalview/io/Jalview2xmlTests.java
index
de12086
..
5b99fa1
100644
(file)
--- a/
test/jalview/io/Jalview2xmlTests.java
+++ b/
test/jalview/io/Jalview2xmlTests.java
@@
-45,6
+45,8
@@
import jalview.gui.JvOptionPane;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.RNAHelicesColour;
import jalview.schemes.TCoffeeColourScheme;
import jalview.structure.StructureImportSettings;
import jalview.viewmodel.AlignmentViewport;
import jalview.schemes.TCoffeeColourScheme;
import jalview.structure.StructureImportSettings;
import jalview.viewmodel.AlignmentViewport;
@@
-64,6
+66,7
@@
import org.testng.annotations.Test;
public class Jalview2xmlTests extends Jalview2xmlBase
{
public class Jalview2xmlTests extends Jalview2xmlBase
{
+ @Override
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
@@
-82,10
+85,10
@@
public class Jalview2xmlTests extends Jalview2xmlBase
assertTrue("Didn't read input file " + inFile, af != null);
int olddsann = countDsAnn(af.getViewport());
assertTrue("Didn't find any dataset annotations", olddsann > 0);
assertTrue("Didn't read input file " + inFile, af != null);
int olddsann = countDsAnn(af.getViewport());
assertTrue("Didn't find any dataset annotations", olddsann > 0);
- af.rnahelicesColour_actionPerformed(null);
- assertTrue(
- "Couldn't apply RNA helices colourscheme",
- af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+ af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices
+ .toString());
+ assertTrue("Couldn't apply RNA helices colourscheme", af.getViewport()
+ .getGlobalColourScheme() instanceof RNAHelicesColour);
assertTrue("Failed to store as a project.",
af.saveAlignment(tfile, FileFormat.Jalview));
af.closeMenuItem_actionPerformed(true);
assertTrue("Failed to store as a project.",
af.saveAlignment(tfile, FileFormat.Jalview));
af.closeMenuItem_actionPerformed(true);
@@
-102,7
+105,7
@@
public class Jalview2xmlTests extends Jalview2xmlBase
+ olddsann + ")");
assertTrue(
"RNA helices colourscheme was not applied on import.",
+ olddsann + ")");
assertTrue(
"RNA helices colourscheme was not applied on import.",
- af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+ af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour);
}
@Test(groups = { "Functional" })
}
@Test(groups = { "Functional" })
@@
-118,9
+121,9
@@
public class Jalview2xmlTests extends Jalview2xmlBase
assertSame("Didn't set T-coffee colourscheme", af.getViewport()
.getGlobalColourScheme().getClass(), TCoffeeColourScheme.class);
assertNotNull("Recognise T-Coffee score from string",
assertSame("Didn't set T-coffee colourscheme", af.getViewport()
.getGlobalColourScheme().getClass(), TCoffeeColourScheme.class);
assertNotNull("Recognise T-Coffee score from string",
- ColourSchemeProperty.getColour(af.getViewport()
- .getAlignment(), ColourSchemeProperty.getColourName(af
- .getViewport().getGlobalColourScheme())));
+ ColourSchemeProperty.getColourScheme(af.getViewport()
+ .getAlignment(), af.getViewport()
+ .getGlobalColourScheme().getSchemeName()));
assertTrue("Failed to store as a project.",
af.saveAlignment(tfile, FileFormat.Jalview));
assertTrue("Failed to store as a project.",
af.saveAlignment(tfile, FileFormat.Jalview));
@@
-160,7
+163,7
@@
public class Jalview2xmlTests extends Jalview2xmlBase
SequenceGroup sg = new SequenceGroup();
sg.setStartRes(57);
sg.setEndRes(92);
SequenceGroup sg = new SequenceGroup();
sg.setStartRes(57);
sg.setEndRes(92);
- sg.cs = gcs;
+ sg.cs.setColourScheme(gcs);
af.getViewport().getAlignment().addGroup(sg);
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
af.getViewport().getAlignment().addGroup(sg);
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
@@
-176,7
+179,7
@@
public class Jalview2xmlTests extends Jalview2xmlBase
ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
- .get(0).cs;
+ .get(0).getColourScheme();
assertNotNull("Didn't recover global colourscheme", _rcs);
assertTrue("Didn't recover annotation colour global scheme",
_rcs instanceof AnnotationColourGradient);
assertNotNull("Didn't recover global colourscheme", _rcs);
assertTrue("Didn't recover annotation colour global scheme",
_rcs instanceof AnnotationColourGradient);
@@
-189,8
+192,8
@@
public class Jalview2xmlTests extends Jalview2xmlBase
for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
&& (!diffseqcols || !diffgseqcols); p++)
{
for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
&& (!diffseqcols || !diffgseqcols); p++)
{
- if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs
- .findColour(sqs[5].getCharAt(p), p, sqs[5]))
+ if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
+ .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
{
diffseqcols = true;
}
{
diffseqcols = true;
}
@@
-209,8
+212,8
@@
public class Jalview2xmlTests extends Jalview2xmlBase
for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
&& (!diffseqcols || !diffgseqcols); p++)
{
for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
&& (!diffseqcols || !diffgseqcols); p++)
{
- if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1]) != _rgcs
- .findColour(sqs[2].getCharAt(p), p, sqs[2]))
+ if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs
+ .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f))
{
diffgseqcols = true;
}
{
diffgseqcols = true;
}
@@
-378,8
+381,8
@@
public class Jalview2xmlTests extends Jalview2xmlBase
Desktop.getAlignFrames().length,
Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
Assert.assertEquals(
Desktop.getAlignFrames().length,
Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
Assert.assertEquals(
- oldviews,
- Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
+ Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
+ oldviews);
}
/**
}
/**