import static org.testng.AssertJUnit.assertEquals;
+import java.awt.Color;
+import java.util.ArrayList;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
+import jalview.gui.OverviewCanvas;
+import jalview.schemes.ColourSchemeI;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import java.awt.Color;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
public class OverviewResColourFinderTest
{
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
}
@Test(groups = { "Functional" })
ResidueColourFinder rcf = new OverviewResColourFinder();
// gaps are grey, residues white
- assertEquals(Color.white, rcf.getResidueColour(av.getResidueShading(),
- null, seq, 0, null));
- assertEquals(Color.lightGray, rcf
- .getResidueColour(av.getResidueShading(), null, seq, 2, null));
-
- // boxes off does not change anything
- av.setShowBoxes(false);
- assertEquals(Color.white, rcf
- .getResidueColour(av.getResidueShading(), null, seq, 0, null));
- assertEquals(Color.lightGray, rcf
- .getResidueColour(av.getResidueShading(),
- null, seq, 2, null));
+ assertEquals(Color.white, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 0, null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 2, null));
+
+ // unaffected by showBoxes setting
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 0, null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 2, null));
}
@Test(groups = { "Functional" })
av.setGlobalColourScheme(new ZappoColourScheme());
// @see ResidueProperties.zappo
- assertEquals(Color.pink, rcf.getResidueColour(av.getResidueShading(),
- null, seq, 0, null)); // M
- assertEquals(Color.green, rcf.getResidueColour(av.getResidueShading(),
- null, seq, 2, null)); // T
- assertEquals(Color.magenta, rcf.getResidueColour(av.getResidueShading(),
- null, seq, 5, null)); // G
- assertEquals(Color.orange, rcf.getResidueColour(av.getResidueShading(),
- null, seq, 12, null)); // F
+ assertEquals(Color.pink, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 0, null)); // M
+ assertEquals(Color.green, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 2, null)); // T
+ assertEquals(Color.magenta, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 5, null)); // G
+ assertEquals(Color.orange, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 12, null)); // F
// gap colour not specified so gaps are lightGray
- assertEquals(Color.lightGray, rcf
- .getResidueColour(av.getResidueShading(), null, seq, 3, null));
-
- // boxes off does not change anything
- av.setShowBoxes(false);
+ assertEquals(Color.lightGray, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 3, null));
- assertEquals(Color.pink, rcf.getResidueColour(av.getResidueShading(),
- null, seq, 0, null)); // M
- assertEquals(Color.green, rcf.getResidueColour(av.getResidueShading(),
- null, seq, 2, null)); // T
- assertEquals(Color.magenta, rcf.getResidueColour(av.getResidueShading(),
- null, seq, 5, null)); // G
- assertEquals(Color.orange, rcf.getResidueColour(av.getResidueShading(),
- null, seq, 12, null)); // F
+ // unaffected by showBoxes setting
+ assertEquals(Color.pink, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 0, null)); // M
+ assertEquals(Color.green, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 2, null)); // T
+ assertEquals(Color.magenta, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 5, null)); // G
+ assertEquals(Color.orange, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 12, null)); // F
// gap colour not specified so gaps are lightGray
- assertEquals(Color.lightGray, rcf
- .getResidueColour(av.getResidueShading(), null, seq, 3, null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 3, null));
}
av.setGlobalColourScheme(new UserColourScheme(newColours));
// gap colour not specified so gaps are lightGray
- assertEquals(Color.lightGray, rcf
- .getResidueColour(av.getResidueShading(), null, seq, 3, null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 3, null));
newColours[23] = Color.pink;
av.setGlobalColourScheme(new UserColourScheme(newColours));
// gap colour specified as pink
- assertEquals(Color.pink, rcf.getResidueColour(av.getResidueShading(),
- null, seq, 3, null));
+ assertEquals(Color.pink, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 3, null));
+
+ // unaffected by showBoxes setting
+ // gap colour not specified so gaps are lightGray
+ newColours[23] = null;
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 3, null));
+
+ newColours[23] = Color.pink;
+ av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+ // gap colour specified as pink
+ assertEquals(Color.pink, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 3, null));
+ }
+
+ @Test
+ public void testGetResidueBoxColour_group()
+ {
+ SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+
+ ColourSchemeI cs = new ZappoColourScheme();
+ ArrayList<SequenceI> seqlist = new ArrayList<>();
+ seqlist.add(seq);
+ SequenceGroup sg = new SequenceGroup(seqlist, "testgroup", cs, true,
+ true, true, 5, 9);
+ al.addGroup(sg);
+ SequenceGroup[] groups = new SequenceGroup[1];
+ groups[0] = sg;
+
+ final AlignViewport av = new AlignViewport(al);
+ ResidueColourFinder rcf = new OverviewResColourFinder();
+
+ // G in group specified as magenta in Zappo
+ assertEquals(Color.magenta, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 7, null));
+
+ // Residue outside group coloured white
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 0, null));
+
+ // Gap outside group coloured lightgray
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 2, null));
+
+ // use legacy colouring
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
+ Color.red);
+
+ // G in group specified as magenta in Zappo
+ assertEquals(Color.magenta, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 7, null));
+
+ // Residue outside group coloured lightgray
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 0, null));
+
+ // Gap outside group coloured white
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 2, null));
+
+ // use new colouring
+ rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
+
+ // G in group specified as magenta in Zappo
+ assertEquals(Color.magenta, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 7, null));
+
+ // Residue outside group coloured white
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 0, null));
+
+ // Gap outside group coloured blue
+ assertEquals(Color.blue, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 2, null));
+ }
+
+ @Test
+ public void testGetBoxColour()
+ {
+ 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();
+ ResidueShaderI shader = new ResidueShader();
+
+ // residues white
+ Color c = rcf.getBoxColour(shader, seq, 0);
+ assertEquals(Color.white, c);
+
+ // gaps gap colour
+ c = rcf.getBoxColour(shader, seq, 3);
+ assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
+
+ // legacy colouring set explicitly via constructor
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
+ Color.red);
+ shader = new ResidueShader();
+
+ // residues light gray
+ c = rcf.getBoxColour(shader, seq, 0);
+ assertEquals(Color.lightGray, c);
+
+ // gaps white
+ c = rcf.getBoxColour(shader, seq, 3);
+ assertEquals(Color.white, c);
+
+ // legacy colouring off
+ rcf = new OverviewResColourFinder();
+ shader = new ResidueShader();
+
+ // residues white
+ c = rcf.getBoxColour(shader, seq, 0);
+ assertEquals(Color.white, c);
+
+ // gaps gap colour
+ c = rcf.getBoxColour(shader, seq, 3);
+ assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
+
+ // non legacy colouring with colour scheme
+ rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
+ shader = new ResidueShader(new ZappoColourScheme());
+
+ // M residue pink
+ c = rcf.getBoxColour(shader, seq, 0);
+ assertEquals(Color.pink, c);
+
+ // gaps blue
+ c = rcf.getBoxColour(shader, seq, 3);
+ assertEquals(Color.blue, c);
+
+ // legacy colouring with colour scheme
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
+ Color.red);
+
+ // M residue pink
+ c = rcf.getBoxColour(shader, seq, 0);
+ assertEquals(Color.pink, c);
+
+ // gaps white
+ c = rcf.getBoxColour(shader, seq, 3);
+ assertEquals(Color.white, c);
}
}
git://source.jalview.org / jalview.git / blobdiff