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Merge branch 'features/JAL-2447experimentalFlag' into develop
[jalview.git]
/
test
/
jalview
/
gui
/
AlignFrameTest.java
diff --git
a/test/jalview/gui/AlignFrameTest.java
b/test/jalview/gui/AlignFrameTest.java
index
8ba165e
..
fed5992
100644
(file)
--- a/
test/jalview/gui/AlignFrameTest.java
+++ b/
test/jalview/gui/AlignFrameTest.java
@@
-85,11
+85,13
@@
public class AlignFrameTest
*/
assertFalse(alignFrame.hideFeatureColumns("exon", true));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
*/
assertFalse(alignFrame.hideFeatureColumns("exon", true));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
- assertTrue(alignFrame.getViewport().getColumnSelection().getHiddenColumns()
+ assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getHiddenRegions()
.isEmpty());
assertFalse(alignFrame.hideFeatureColumns("exon", false));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
.isEmpty());
assertFalse(alignFrame.hideFeatureColumns("exon", false));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
- assertTrue(alignFrame.getViewport().getColumnSelection().getHiddenColumns()
+ assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getHiddenRegions()
.isEmpty());
/*
.isEmpty());
/*
@@
-97,8
+99,9
@@
public class AlignFrameTest
*/
assertFalse(alignFrame.hideFeatureColumns("Metal", true));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
*/
assertFalse(alignFrame.hideFeatureColumns("Metal", true));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
- List<int[]> hidden = alignFrame.getViewport().getColumnSelection()
- .getHiddenColumns();
+ List<int[]> hidden = alignFrame.getViewport().getAlignment()
+ .getHiddenColumns()
+ .getHiddenRegions();
assertTrue(hidden.isEmpty());
/*
assertTrue(hidden.isEmpty());
/*
@@
-107,7
+110,8
@@
public class AlignFrameTest
* [1-3], [6-8] base zero
*/
assertTrue(alignFrame.hideFeatureColumns("Turn", true));
* [1-3], [6-8] base zero
*/
assertTrue(alignFrame.hideFeatureColumns("Turn", true));
- hidden = alignFrame.getViewport().getColumnSelection().getHiddenColumns();
+ hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getHiddenRegions();
assertEquals(hidden.size(), 2);
assertEquals(hidden.get(0)[0], 1);
assertEquals(hidden.get(0)[1], 3);
assertEquals(hidden.size(), 2);
assertEquals(hidden.get(0)[0], 1);
assertEquals(hidden.get(0)[1], 3);
@@
-183,8
+187,8
@@
public class AlignFrameTest
af.applyToAllGroups_actionPerformed(false);
af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
af.applyToAllGroups_actionPerformed(false);
af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
- assertFalse(av.getViewportColourScheme().conservationApplied());
- assertEquals(av.getViewportColourScheme().getThreshold(), 0);
+ assertFalse(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getThreshold(), 0);
/*
* Apply Conservation 20%
/*
* Apply Conservation 20%
@@
-196,8
+200,8
@@
public class AlignFrameTest
new String[] { "Background" }));
assertTrue(sp.isForConservation());
sp.valueChanged(20);
new String[] { "Background" }));
assertTrue(sp.isForConservation());
sp.valueChanged(20);
- assertTrue(av.getViewportColourScheme().conservationApplied());
- assertEquals(av.getViewportColourScheme().getConservationInc(), 20);
+ assertTrue(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getConservationInc(), 20);
/*
* Apply PID threshold 10% (conservation still applies as well)
/*
* Apply PID threshold 10% (conservation still applies as well)
@@
-209,9
+213,9
@@
public class AlignFrameTest
"label.percentage_identity_threshold",
new String[] { "Background" }));
sp.valueChanged(10);
"label.percentage_identity_threshold",
new String[] { "Background" }));
sp.valueChanged(10);
- assertEquals(av.getViewportColourScheme().getThreshold(), 10);
- assertTrue(av.getViewportColourScheme().conservationApplied());
- assertEquals(av.getViewportColourScheme().getConservationInc(), 20);
+ assertEquals(av.getResidueShading().getThreshold(), 10);
+ assertTrue(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getConservationInc(), 20);
/*
* create a group with Strand colouring, 30% Conservation
/*
* create a group with Strand colouring, 30% Conservation
@@
-263,9
+267,9
@@
public class AlignFrameTest
*/
af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString());
assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme);
*/
af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString());
assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme);
- assertTrue(av.getViewportColourScheme().conservationApplied());
- assertEquals(av.getViewportColourScheme().getConservationInc(), 20);
- assertEquals(av.getViewportColourScheme().getThreshold(), 10);
+ assertTrue(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getConservationInc(), 20);
+ assertEquals(av.getResidueShading().getThreshold(), 10);
assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
assertTrue(sg.getGroupColourScheme().conservationApplied());
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
assertTrue(sg.getGroupColourScheme().conservationApplied());
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
@@
-278,9
+282,9
@@
public class AlignFrameTest
af.applyToAllGroups_actionPerformed(true);
af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
af.applyToAllGroups_actionPerformed(true);
af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
- assertTrue(av.getViewportColourScheme().conservationApplied());
- assertEquals(av.getViewportColourScheme().getConservationInc(), 20);
- assertEquals(av.getViewportColourScheme().getThreshold(), 10);
+ assertTrue(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getConservationInc(), 20);
+ assertEquals(av.getResidueShading().getThreshold(), 10);
assertTrue(sg.getColourScheme() instanceof HelixColourScheme);
assertTrue(sg.getGroupColourScheme().conservationApplied());
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
assertTrue(sg.getColourScheme() instanceof HelixColourScheme);
assertTrue(sg.getGroupColourScheme().conservationApplied());
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
@@
-314,8
+318,8
@@
public class AlignFrameTest
af.applyToAllGroups_actionPerformed(false);
af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
af.applyToAllGroups_actionPerformed(false);
af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString());
assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme);
- assertFalse(av.getViewportColourScheme().conservationApplied());
- assertEquals(av.getViewportColourScheme().getThreshold(), 0);
+ assertFalse(av.getResidueShading().conservationApplied());
+ assertEquals(av.getResidueShading().getThreshold(), 0);
/*
* inspect the colour of
/*
* inspect the colour of
@@
-323,7
+327,7
@@
public class AlignFrameTest
* FER_CAPAN.10(SER), column 16 (15 base 0)
*/
SequenceI ferCapan = al.findName("FER_CAPAN");
* FER_CAPAN.10(SER), column 16 (15 base 0)
*/
SequenceI ferCapan = al.findName("FER_CAPAN");
- ResidueShaderI rs = av.getViewportColourScheme();
+ ResidueShaderI rs = av.getResidueShading();
Color c = rs.findColour('I', 14, ferCapan);
Color i_original = new Color(138, 117, 138);
assertEquals(c, i_original);
Color c = rs.findColour('I', 14, ferCapan);
Color i_original = new Color(138, 117, 138);
assertEquals(c, i_original);
@@
-339,7
+343,7
@@
public class AlignFrameTest
assertTrue(sp.isForConservation());
assertEquals(sp.getValue(), 30); // initial slider setting
sp.valueChanged(10);
assertTrue(sp.isForConservation());
assertEquals(sp.getValue(), 30); // initial slider setting
sp.valueChanged(10);
- assertSame(rs, av.getViewportColourScheme());
+ assertSame(rs, av.getResidueShading());
c = rs.findColour('I', 14, ferCapan);
Color i_faded = new Color(196, 186, 196);
assertEquals(c, i_faded);
c = rs.findColour('I', 14, ferCapan);
Color i_faded = new Color(196, 186, 196);
assertEquals(c, i_faded);
@@
-490,7
+494,7
@@
public class AlignFrameTest
sp = SliderPanel.getSliderPanel();
assertTrue(sp.isForConservation());
sp.valueChanged(20);
sp = SliderPanel.getSliderPanel();
assertTrue(sp.isForConservation());
sp.valueChanged(20);
- ResidueShaderI rs = av.getViewportColourScheme();
+ ResidueShaderI rs = av.getResidueShading();
assertEquals(rs.getThreshold(), 10);
assertTrue(rs.conservationApplied());
assertEquals(rs.getConservationInc(), 20);
assertEquals(rs.getThreshold(), 10);
assertTrue(rs.conservationApplied());
assertEquals(rs.getConservationInc(), 20);
@@
-540,8
+544,8
@@
public class AlignFrameTest
assertEquals(af.alignPanel.getViewName(), "View 1");
AlignViewport av2 = af.getViewport();
assertNotSame(av, av2);
assertEquals(af.alignPanel.getViewName(), "View 1");
AlignViewport av2 = af.getViewport();
assertNotSame(av, av2);
- rs = av2.getViewportColourScheme();
- assertNotSame(av.getViewportColourScheme(), rs);
+ rs = av2.getResidueShading();
+ assertNotSame(av.getResidueShading(), rs);
assertEquals(rs.getThreshold(), 10);
assertTrue(rs.conservationApplied());
assertEquals(rs.getConservationInc(), 20);
assertEquals(rs.getThreshold(), 10);
assertTrue(rs.conservationApplied());
assertEquals(rs.getConservationInc(), 20);
@@
-562,6
+566,6
@@
public class AlignFrameTest
"label.conservation_colour_increment",
new String[] { "View 1" }));
sp.valueChanged(22);
"label.conservation_colour_increment",
new String[] { "View 1" }));
sp.valueChanged(22);
- assertEquals(av2.getViewportColourScheme().getConservationInc(), 22);
+ assertEquals(av2.getResidueShading().getConservationInc(), 22);
}
}
}
}