JAL-4090 JAL-4218 patch and release notes - don’t include dist in tarball

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

diff --git a/test/jalview/schemes/ColourSchemePropertyTest.java b/test/jalview/schemes/ColourSchemePropertyTest.java
index efea164..ee65819 100644 (file)
--- a/test/jalview/schemes/ColourSchemePropertyTest.java
+++ b/test/jalview/schemes/ColourSchemePropertyTest.java
@@ -1,17 +1,41 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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
+  @Test(groups = "Functional")
   public void testGetColourName()
   {
     SequenceI seq = new Sequence("Seq1", "abcd");
@@ -65,4 +89,70 @@ public class ColourSchemePropertyTest
 
     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(null, al,
+            "Clustal");
+    assertTrue(cs instanceof ClustalxColourScheme);
+    // not case-sensitive
+    cs = ColourSchemeProperty.getColourScheme(null, al, "CLUSTAL");
+    assertTrue(cs instanceof ClustalxColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "clustal");
+    assertTrue(cs instanceof ClustalxColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Blosum62");
+    assertTrue(cs instanceof Blosum62ColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "% Identity");
+    assertTrue(cs instanceof PIDColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Zappo");
+    assertTrue(cs instanceof ZappoColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Taylor");
+    assertTrue(cs instanceof TaylorColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Hydrophobic");
+    assertTrue(cs instanceof HydrophobicColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Helix Propensity");
+    assertTrue(cs instanceof HelixColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al,
+            "Strand Propensity");
+    assertTrue(cs instanceof StrandColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Turn Propensity");
+    assertTrue(cs instanceof TurnColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Buried Index");
+    assertTrue(cs instanceof BuriedColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "Nucleotide");
+    assertTrue(cs instanceof NucleotideColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al,
+            "Purine/Pyrimidine");
+    assertTrue(cs instanceof PurinePyrimidineColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "T-Coffee Scores");
+    assertTrue(cs instanceof TCoffeeColourScheme);
+    cs = ColourSchemeProperty.getColourScheme(null, al, "RNA Helices");
+    assertTrue(cs instanceof RNAHelicesColour);
+    // 'None' is a special value
+    assertNull(ColourSchemeProperty.getColourScheme(null, al, "None"));
+    assertNull(ColourSchemeProperty.getColourScheme(null, al, "none"));
+    // default is to convert the name into a fixed colour
+    cs = ColourSchemeProperty.getColourScheme(null, al, "elephants");
+    assertTrue(cs instanceof UserColourScheme);
+
+    /*
+     * explicit aa colours
+     */
+    UserColourScheme ucs = (UserColourScheme) ColourSchemeProperty
+            .getColourScheme(null, 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));
+  }
 }