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
JAL-2629 fix hmsearch and jackhmmer not being able to search alignment
[jalview.git]
/
test
/
jalview
/
renderer
/
OverviewResColourFinderTest.java
diff --git
a/test/jalview/renderer/OverviewResColourFinderTest.java
b/test/jalview/renderer/OverviewResColourFinderTest.java
index
2016087
..
d01e53f
100644
(file)
--- a/
test/jalview/renderer/OverviewResColourFinderTest.java
+++ b/
test/jalview/renderer/OverviewResColourFinderTest.java
@@
-22,6
+22,7
@@
package jalview.renderer;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertEquals;
+import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
@@
-30,10
+31,10
@@
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
-import jalview.gui.Preferences;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
import java.util.ArrayList;
import java.awt.Color;
import java.util.ArrayList;
@@
-57,7
+58,7
@@
public class OverviewResColourFinderTest
{
SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
AlignmentI al = new Alignment(new SequenceI[] { seq });
{
SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new OverviewResColourFinder();
// gaps are grey, residues white
ResidueColourFinder rcf = new OverviewResColourFinder();
// gaps are grey, residues white
@@
-81,7
+82,7
@@
public class OverviewResColourFinderTest
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
AlignmentI al = new Alignment(new SequenceI[] { seq });
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new OverviewResColourFinder();
av.setGlobalColourScheme(new ZappoColourScheme());
ResidueColourFinder rcf = new OverviewResColourFinder();
av.setGlobalColourScheme(new ZappoColourScheme());
@@
-127,7
+128,7
@@
public class OverviewResColourFinderTest
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
AlignmentI al = new Alignment(new SequenceI[] { seq });
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new OverviewResColourFinder();
Color[] newColours = new Color[24];
ResidueColourFinder rcf = new OverviewResColourFinder();
Color[] newColours = new Color[24];
@@
-180,7
+181,7
@@
public class OverviewResColourFinderTest
SequenceGroup[] groups = new SequenceGroup[1];
groups[0] = sg;
SequenceGroup[] groups = new SequenceGroup[1];
groups[0] = sg;
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new OverviewResColourFinder();
// G in group specified as magenta in Zappo
ResidueColourFinder rcf = new OverviewResColourFinder();
// G in group specified as magenta in Zappo
@@
-231,8
+232,6
@@
public class OverviewResColourFinderTest
{
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
{
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
- AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
// non-legacy colouring
ResidueColourFinder rcf = new OverviewResColourFinder();
// non-legacy colouring
ResidueColourFinder rcf = new OverviewResColourFinder();
@@
-244,7
+243,9
@@
public class OverviewResColourFinderTest
// gaps gap colour
c = rcf.getBoxColour(shader, seq, 3);
// gaps gap colour
c = rcf.getBoxColour(shader, seq, 3);
- assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+ assertEquals(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
+ c);
// legacy colouring set explicitly via constructor
rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
// legacy colouring set explicitly via constructor
rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
@@
-268,7
+269,7
@@
public class OverviewResColourFinderTest
// gaps gap colour
c = rcf.getBoxColour(shader, seq, 3);
// gaps gap colour
c = rcf.getBoxColour(shader, seq, 3);
- assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+ assertEquals(OverviewResColourFinder.OVERVIEW_DEFAULT_GAP, c);
// non legacy colouring with colour scheme
rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
// non legacy colouring with colour scheme
rcf = new OverviewResColourFinder(false, Color.blue, Color.red);