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 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112
[jalview.git]
/
test
/
jalview
/
schemes
/
PIDColourSchemeTest.java
diff --git
a/test/jalview/schemes/PIDColourSchemeTest.java
b/test/jalview/schemes/PIDColourSchemeTest.java
index
8bab428
..
4117b23
100644
(file)
--- a/
test/jalview/schemes/PIDColourSchemeTest.java
+++ b/
test/jalview/schemes/PIDColourSchemeTest.java
@@
-2,15
+2,15
@@
package jalview.schemes;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertEquals;
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-
-import java.awt.Color;
-
-import org.testng.annotations.Test;
+import jalview.viewmodel.AlignmentViewport;
public class PIDColourSchemeTest
{
public class PIDColourSchemeTest
{
@@
-42,6
+42,7
@@
public class PIDColourSchemeTest
/*
* doesn't use column or sequence
/*
* doesn't use column or sequence
+ * we assume consensus residue is computed as upper case
*/
assertEquals(scheme.findColour('A', 0, null, "A", 0f), white);
assertEquals(scheme.findColour('A', 0, null, "A", 40f), white);
*/
assertEquals(scheme.findColour('A', 0, null, "A", 0f), white);
assertEquals(scheme.findColour('A', 0, null, "A", 40f), white);
@@
-54,8
+55,6
@@
public class PIDColourSchemeTest
assertEquals(scheme.findColour('A', 0, null, "KFV", 100f), white);
assertEquals(scheme.findColour('a', 0, null, "A", 80f), over60);
assertEquals(scheme.findColour('A', 0, null, "KFV", 100f), white);
assertEquals(scheme.findColour('a', 0, null, "A", 80f), over60);
- assertEquals(scheme.findColour('A', 0, null, "a", 80f), over60);
- assertEquals(scheme.findColour('a', 0, null, "a", 80f), over60);
assertEquals(scheme.findColour('A', 0, null, "AC", 80f), over60);
assertEquals(scheme.findColour('A', 0, null, "KCA", 80f), over60);
}
assertEquals(scheme.findColour('A', 0, null, "AC", 80f), over60);
assertEquals(scheme.findColour('A', 0, null, "KCA", 80f), over60);
}
@@
-78,10
+77,23
@@
public class PIDColourSchemeTest
* first column PID is 50%, or 67% ignoring gaps
*/
String seqs = ">seq1\nAAAAA\n>seq2\nAAAAA\n>seq3\n-CCCC\n>seq4\nFFFFF\n";
* first column PID is 50%, or 67% ignoring gaps
*/
String seqs = ">seq1\nAAAAA\n>seq2\nAAAAA\n>seq3\n-CCCC\n>seq4\nFFFFF\n";
+
+ /*
+ * load data and wait for consensus to be computed
+ */
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
DataSourceType.PASTE);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
DataSourceType.PASTE);
- AlignViewport viewport = af.getViewport();
+ AlignmentViewport viewport = af.getViewport();
viewport.setIgnoreGapsConsensus(false, af.alignPanel);
viewport.setIgnoreGapsConsensus(false, af.alignPanel);
+ do
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ } while (af.getViewport().getCalcManager().isWorking());
af.changeColour_actionPerformed(JalviewColourScheme.PID.toString());
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
af.changeColour_actionPerformed(JalviewColourScheme.PID.toString());
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
@@
-90,7
+102,7
@@
public class PIDColourSchemeTest
* including gaps, A should be coloured for 50% consensus
*/
Color c = viewport
* including gaps, A should be coloured for 50% consensus
*/
Color c = viewport
- .getViewportColourScheme().findColour('A', 0, seq);
+ .getResidueShading().findColour('A', 0, seq);
assertEquals(c, over40);
/*
assertEquals(c, over40);
/*
@@
-98,7
+110,7
@@
public class PIDColourSchemeTest
*/
viewport.setIgnoreGapsConsensus(true, af.alignPanel);
c = viewport
*/
viewport.setIgnoreGapsConsensus(true, af.alignPanel);
c = viewport
- .getViewportColourScheme().findColour('A', 0, seq);
+ .getResidueShading().findColour('A', 0, seq);
assertEquals(c, over60);
}
}
assertEquals(c, over60);
}
}