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.api.AlignViewportI; 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(AlignViewportI view, AnnotatedCollectionI sg) { 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 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(AlignViewportI view, AnnotatedCollectionI sg) { return new MyClustal(sg, view.getHiddenRepSequences()); } @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 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.getResidueColour(seq, 88, null); // E 255,0,102 Color taylor2 = sr.getResidueColour(seq, 89, null); // A 204,255,0 Color taylor3 = sr.getResidueColour(seq, 90, null); // 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.getResidueColour(seq, 88, null); // E red Color zappo2 = sr.getResidueColour(seq, 89, null); // A pink Color zappo3 = sr.getResidueColour(seq, 90, null); // 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.getResidueColour(seq, 88, null); Color stripy2 = sr.getResidueColour(seq, 89, null); Color stripy3 = sr.getResidueColour(seq, 90, null); assertEquals(stripy1, zappo1); assertEquals(stripy2, taylor2); assertEquals(stripy3, zappo3); /* * set and check Clustal colours */ af.changeColour_actionPerformed(JalviewColourScheme.Clustal.toString()); Color clustal1 = sr.getResidueColour(seq, 88, null); Color clustal2 = sr.getResidueColour(seq, 89, null); Color clustal3 = sr.getResidueColour(seq, 90, null); 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.getResidueColour(seq, 88, null); Color myclustal2 = sr.getResidueColour(seq, 89, null); Color myclustal3 = sr.getResidueColour(seq, 90, null); 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")); } }