Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / test / jalview / schemes / ColourSchemePropertyTest.java

diff --git a/test/jalview/schemes/ColourSchemePropertyTest.java b/test/jalview/schemes/ColourSchemePropertyTest.java
new file mode 100644 (file)
index 0000000..11562b8
--- /dev/null
+++ b/test/jalview/schemes/ColourSchemePropertyTest.java
@@ -0,0 +1,135 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class ColourSchemePropertyTest
+{
+  @Test(groups = "Functional")
+  public void testGetColourName()
+  {
+    SequenceI seq = new Sequence("Seq1", "abcd");
+    AlignmentI al = new Alignment(new SequenceI[] { seq });
+    ColourSchemeI cs = new ClustalxColourScheme(al, null);
+    assertEquals(ColourSchemeProperty.getColourName(cs), "Clustal");
+    cs = new Blosum62ColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs), "Blosum62");
+    cs = new PIDColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs), "% Identity");
+    cs = new HydrophobicColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs), "Hydrophobic");
+    cs = new ZappoColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs), "Zappo");
+    cs = new TaylorColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs), "Taylor");
+    cs = new HelixColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs),
+            "Helix Propensity");
+    cs = new StrandColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs),
+            "Strand Propensity");
+    cs = new TurnColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs), "Turn Propensity");
+    cs = new BuriedColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs), "Buried Index");
+    cs = new NucleotideColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs), "Nucleotide");
+    cs = new PurinePyrimidineColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs),
+            "Purine/Pyrimidine");
+    cs = new TCoffeeColourScheme(al);
+    assertEquals(ColourSchemeProperty.getColourName(cs), "T-Coffee Scores");
+    cs = new RNAHelicesColour(al);
+    assertEquals(ColourSchemeProperty.getColourName(cs), "RNA Helices");
+    cs = new RNAInteractionColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs),
+            "RNA Interaction type");
+    cs = new UserColourScheme();
+    assertEquals(ColourSchemeProperty.getColourName(cs), "User Defined");
+
+    /*
+     * UserColourScheme may have a bespoke name
+     */
+    ((UserColourScheme) cs).setName("stripy");
+    assertEquals(ColourSchemeProperty.getColourName(cs), "stripy");
+    ((UserColourScheme) cs).setName("");
+    assertEquals(ColourSchemeProperty.getColourName(cs), "User Defined");
+    ((UserColourScheme) cs).setName(null);
+    assertEquals(ColourSchemeProperty.getColourName(cs), "User Defined");
+
+    assertEquals(ColourSchemeProperty.getColourName(null), "None");
+  }
+
+  @Test(groups = "Functional")
+  public void testGetColourScheme()
+  {
+    SequenceI seq = new Sequence("Seq1", "abcd");
+    AlignmentI al = new Alignment(new SequenceI[] { seq });
+    // the strings here correspond to JalviewColourScheme.toString() values
+    ColourSchemeI cs = ColourSchemeProperty.getColourScheme(al, "Clustal");
+    assertTrue(cs instanceof ClustalxColourScheme);
+    // not case-sensitive
+    cs = ColourSchemeProperty.getColourScheme(al, "CLUSTAL");
+    assertTrue(cs instanceof ClustalxColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "clustal");
+    assertTrue(cs instanceof ClustalxColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "Blosum62");
+    assertTrue(cs instanceof Blosum62ColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "% Identity");
+    assertTrue(cs instanceof PIDColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "Zappo");
+    assertTrue(cs instanceof ZappoColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "Taylor");
+    assertTrue(cs instanceof TaylorColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "Hydrophobic");
+    assertTrue(cs instanceof HydrophobicColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "Helix Propensity");
+    assertTrue(cs instanceof HelixColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "Strand Propensity");
+    assertTrue(cs instanceof StrandColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "Turn Propensity");
+    assertTrue(cs instanceof TurnColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "Buried Index");
+    assertTrue(cs instanceof BuriedColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "Nucleotide");
+    assertTrue(cs instanceof NucleotideColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "Purine/Pyrimidine");
+    assertTrue(cs instanceof PurinePyrimidineColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "T-Coffee Scores");
+    assertTrue(cs instanceof TCoffeeColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(al, "RNA Helices");
+    assertTrue(cs instanceof RNAHelicesColour);
+    // 'None' is a special value
+    assertNull(ColourSchemeProperty.getColourScheme(al, "None"));
+    assertNull(ColourSchemeProperty.getColourScheme(al, "none"));
+    // default is to convert the name into a fixed colour
+    cs = ColourSchemeProperty.getColourScheme(al, "elephants");
+    assertTrue(cs instanceof UserColourScheme);
+
+    /*
+     * explicit aa colours
+     */
+    UserColourScheme ucs = (UserColourScheme) ColourSchemeProperty
+            .getColourScheme(al,
+            "R,G=red;C=blue;c=green;Q=10,20,30;S,T=11ffdd");
+    assertEquals(ucs.findColour('H'), Color.white);
+    assertEquals(ucs.findColour('R'), Color.red);
+    assertEquals(ucs.findColour('r'), Color.red);
+    assertEquals(ucs.findColour('G'), Color.red);
+    assertEquals(ucs.findColour('C'), Color.blue);
+    assertEquals(ucs.findColour('c'), Color.green);
+    assertEquals(ucs.findColour('Q'), new Color(10, 20, 30));
+    assertEquals(ucs.findColour('S'), new Color(0x11ffdd));
+    assertEquals(ucs.findColour('T'), new Color(0x11ffdd));
+  }
+}