*/
assertFalse(alignFrame.hideFeatureColumns("exon", true));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
- assertTrue(alignFrame.getViewport().getColumnSelection().getHiddenColumns()
+ assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy()
.isEmpty());
assertFalse(alignFrame.hideFeatureColumns("exon", false));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
- assertTrue(alignFrame.getViewport().getColumnSelection().getHiddenColumns()
+ assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy()
.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()
+ .getHiddenColumnsCopy();
assertTrue(hidden.isEmpty());
/*
* [1-3], [6-8] base zero
*/
assertTrue(alignFrame.hideFeatureColumns("Turn", true));
- hidden = alignFrame.getViewport().getColumnSelection().getHiddenColumns();
+ hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy();
assertEquals(hidden.size(), 2);
assertEquals(hidden.get(0)[0], 1);
assertEquals(hidden.get(0)[1], 3);
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%
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)
"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
*/
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);
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);
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
* 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);
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);
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(af.alignPanel.getViewName(), "View 1");
AlignViewport av2 = af.getViewport();
assertNotSame(av, av2);
- rs = av2.getViewportColourScheme();
- assertNotSame(av.getViewportColourScheme(), rs);
+ assertSame(av2, af.alignPanel.av);
+ rs = av2.getResidueShading();
+ assertNotSame(av.getResidueShading(), rs);
assertEquals(rs.getThreshold(), 10);
- assertTrue(rs.conservationApplied());
+ assertTrue(rs.conservationApplied(), rs.toString());
assertEquals(rs.getConservationInc(), 20);
assertEquals(av2.getAlignment().getGroups().size(), 1);
sg = av2.getAlignment().getGroups().get(0);
"label.conservation_colour_increment",
new String[] { "View 1" }));
sp.valueChanged(22);
- assertEquals(av2.getViewportColourScheme().getConservationInc(), 22);
+ assertEquals(av2.getResidueShading().getConservationInc(), 22);
}
}