--- /dev/null
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertSame;
+import static org.testng.Assert.assertTrue;
+
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.SequenceRenderer;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.schemes.ClustalxColourScheme.ClustalColour;
+
+import java.awt.Color;
+import java.util.Iterator;
+import java.util.Map;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class ColourSchemesTest
+{
+ /*
+ * a colour scheme that alternates Taylor and Zappo
+ * colouring by column
+ */
+ class Stripy extends ResidueColourScheme
+ {
+ private ResidueColourScheme odd;
+
+ private ResidueColourScheme even;
+
+ private Stripy()
+ {
+ }
+
+ /**
+ * constructor given colours for odd and even columns
+ *
+ * @param odd
+ * @param even
+ */
+ private Stripy(ColourSchemeI cs1, ColourSchemeI cs2)
+ {
+ odd = (ResidueColourScheme) cs1;
+ even = (ResidueColourScheme) cs2;
+ }
+
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ final ColourSchemeI cs1 = ColourSchemes.getInstance()
+ .getColourScheme(JalviewColourScheme.Taylor.toString(),
+ (AnnotatedCollectionI) null);
+ final ColourSchemeI cs2 = ColourSchemes.getInstance()
+ .getColourScheme(JalviewColourScheme.Zappo.toString(),
+ (AnnotatedCollectionI) null);
+ return new Stripy(cs1, cs2);
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ if (j % 2 == 1)
+ {
+ return odd.findColour(c, j, seq);
+ }
+ else
+ {
+ return even.findColour(c, j, seq);
+ }
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "stripy";
+ }
+ };
+
+ /*
+ * a colour scheme that is Clustal but using AWT colour equivalents
+ */
+ class MyClustal extends ResidueColourScheme
+ {
+ ClustalxColourScheme delegate;
+
+ private MyClustal()
+ {
+ }
+
+ private MyClustal(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ delegate = new ClustalxColourScheme(sg, hiddenRepSequences);
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ Color col = delegate.findColour(c, j, seq);
+ Color result = col;
+ if (col.equals(ClustalColour.BLUE.colour))
+ {
+ result = Color.blue;
+ }
+ else if (col.equals(ClustalColour.CYAN.colour))
+ {
+ result = Color.cyan;
+ }
+ else if (col.equals(ClustalColour.GREEN.colour))
+ {
+ result = Color.green;
+ }
+ else if (col.equals(ClustalColour.MAGENTA.colour))
+ {
+ result = Color.magenta;
+ }
+ else if (col.equals(ClustalColour.ORANGE.colour))
+ {
+ result = Color.orange;
+ }
+ else if (col.equals(ClustalColour.PINK.colour))
+ {
+ result = Color.pink;
+ }
+ else if (col.equals(ClustalColour.RED.colour))
+ {
+ result = Color.red;
+ }
+ else if (col.equals(ClustalColour.YELLOW.colour))
+ {
+ result = Color.yellow;
+ }
+ return result;
+ }
+
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ return new MyClustal(sg, hiddenRepSequences);
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "MyClustal";
+ }
+
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Jalview.main(new String[] { "-nonews" });
+ }
+
+ @AfterClass(alwaysRun = true)
+ public static void tearDownAfterClass() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourSchemes()
+ {
+ /*
+ * this just verifies that built-in colour schemes are loaded into ColourSchemes
+ * in the order in which they are declared in the JalviewColourScheme enum
+ * (this also determines their order in Colour menus)
+ */
+ Iterator<ColourSchemeI> schemes = ColourSchemes.getInstance().getColourSchemes().iterator();
+ JalviewColourScheme[] jalviewSchemes = JalviewColourScheme.values();
+ int i = 0;
+ while (schemes.hasNext() && i < jalviewSchemes.length)
+ {
+ assertTrue(schemes.next().getSchemeName()
+ .equals(jalviewSchemes[i].toString()));
+ i++;
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourScheme()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">seq1\nAGLRTWQU", DataSourceType.PASTE);
+ ColourSchemes schemes = ColourSchemes.getInstance();
+
+ AnnotatedCollectionI al = af.getViewport().getAlignment();
+
+ for (JalviewColourScheme cs : JalviewColourScheme.values())
+ {
+ ColourSchemeI registered = schemes.getColourScheme(cs.toString(), al);
+ assertSame(registered.getClass(), cs.getSchemeClass());
+ }
+ af.closeMenuItem_actionPerformed(true);
+ }
+
+ @Test(groups = "Functional")
+ public void testRegisterColourScheme()
+ {
+ ColourSchemes.getInstance().registerColourScheme(new Stripy());
+ ColourSchemes.getInstance().registerColourScheme(new MyClustal());
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ /*
+ * set a breakpoint here to see and play with the newly registered
+ * colour schemes in the AlignFrame colour menu
+ */
+ SequenceRenderer sr = new SequenceRenderer(af.getViewport());
+ SequenceI seq = af.getViewport().getAlignment().findName("FER_CAPAA");
+
+ /*
+ * set and check Taylor colours
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Taylor.toString());
+ Color taylor1 = sr.getResidueBoxColour(seq, 88); // E 255,0,102
+ Color taylor2 = sr.getResidueBoxColour(seq, 89); // A 204,255,0
+ Color taylor3 = sr.getResidueBoxColour(seq, 90); // G 255,153,0
+ assertEquals(taylor1, new Color(255, 0, 102));
+ assertEquals(taylor2, new Color(204, 255, 0));
+ assertEquals(taylor3, new Color(255, 153, 0));
+
+ /*
+ * set and check Zappo colours
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Zappo.toString());
+ Color zappo1 = sr.getResidueBoxColour(seq, 88); // E red
+ Color zappo2 = sr.getResidueBoxColour(seq, 89); // A pink
+ Color zappo3 = sr.getResidueBoxColour(seq, 90); // G magenta
+ assertEquals(zappo1, Color.red);
+ assertEquals(zappo2, Color.pink);
+ assertEquals(zappo3, Color.magenta);
+
+ /*
+ * set 'stripy' colours - odd columns are Taylor and even are Zappo
+ */
+ af.changeColour_actionPerformed("stripy");
+ Color stripy1 = sr.getResidueBoxColour(seq, 88);
+ Color stripy2 = sr.getResidueBoxColour(seq, 89);
+ Color stripy3 = sr.getResidueBoxColour(seq, 90);
+ assertEquals(stripy1, zappo1);
+ assertEquals(stripy2, taylor2);
+ assertEquals(stripy3, zappo3);
+
+ /*
+ * set and check Clustal colours
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Clustal.toString());
+ Color clustal1 = sr.getResidueBoxColour(seq, 88);
+ Color clustal2 = sr.getResidueBoxColour(seq, 89);
+ Color clustal3 = sr.getResidueBoxColour(seq, 90);
+ assertEquals(clustal1, ClustalColour.MAGENTA.colour);
+ assertEquals(clustal2, ClustalColour.BLUE.colour);
+ assertEquals(clustal3, ClustalColour.ORANGE.colour);
+
+ /*
+ * set 'MyClustal' colours - uses AWT colour equivalents
+ */
+ af.changeColour_actionPerformed("MyClustal");
+ Color myclustal1 = sr.getResidueBoxColour(seq, 88);
+ Color myclustal2 = sr.getResidueBoxColour(seq, 89);
+ Color myclustal3 = sr.getResidueBoxColour(seq, 90);
+ assertEquals(myclustal1, Color.MAGENTA);
+ assertEquals(myclustal2, Color.BLUE);
+ assertEquals(myclustal3, Color.ORANGE);
+ }
+
+ /**
+ * Tests for check if scheme name exists. Built-in scheme names are the
+ * toString() values of enum JalviewColourScheme.
+ */
+ @Test(groups = "Functional")
+ public void testNameExists()
+ {
+ ColourSchemes cs = ColourSchemes.getInstance();
+ assertFalse(cs.nameExists(null));
+ assertFalse(cs.nameExists(""));
+ assertTrue(cs.nameExists("Clustal"));
+ assertTrue(cs.nameExists("CLUSTAL"));
+ assertFalse(cs.nameExists("CLUSTAL "));
+ assertTrue(cs.nameExists("% Identity"));
+ assertFalse(cs.nameExists("PID"));
+ }
+}
git://source.jalview.org / jalview.git / blobdiff