X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FClustalxColourSchemeTest.java;h=6731465dbdad4d02b04ef355337f883cb90d641c;hb=e9a1c2c372f4bbf6cf658de3dba73ef326b20c20;hp=16317d94acbdcb7a74fbfb26b0ac3382d9c5a831;hpb=db371136969ed3f5b7a6b08b431e53fc752f30e7;p=jalview.git

diff --git a/test/jalview/schemes/ClustalxColourSchemeTest.java b/test/jalview/schemes/ClustalxColourSchemeTest.java
index 16317d9..6731465 100644
--- a/test/jalview/schemes/ClustalxColourSchemeTest.java
+++ b/test/jalview/schemes/ClustalxColourSchemeTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -27,13 +47,13 @@ public class ClustalxColourSchemeTest
           ">seq0\nKKKWWWQW\n";
   // @formatter:on
 
-  @Test
+  @Test(groups = "Functional")
   public void testFindColour()
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(FASTA,
             DataSourceType.PASTE);
     AlignmentI al = af.getViewport().getAlignment();
-    ColourSchemeI cs = new ClustalxColourScheme(al, null);
+    ClustalxColourScheme cs = new ClustalxColourScheme(al, null);
 
     /*
      * column 1 is 70% A which is above Clustalx threshold of 60%
@@ -85,4 +105,50 @@ public class ClustalxColourSchemeTest
 
     // TODO more test cases; check if help documentation matches implementation
   }
+
+  // @formatter:on
+
+  /**
+   * Test for colour calculation when the consensus percentage ignores gapped
+   * sequences
+   */
+  @Test(groups = "Functional")
+  public void testFindColour_ignoreGaps()
+  {
+    /*
+     * CCC
+     * CCC
+     * -CC
+     * first column is 66% C (blue) including gaps
+     * or 100% C ignoring gaps
+     */
+    String fasta = ">seq1\nCCC\n>seq2\nccc\n>seq3\n-CC\n";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
+            DataSourceType.PASTE);
+    AlignmentI al = af.getViewport().getAlignment();
+    ClustalxColourScheme cs = new ClustalxColourScheme(al, null);
+
+    /*
+     * column 1 is 66% C which is above Clustalx threshold of 60%
+     */
+    Color clustalBlue = ClustalxColourScheme.ClustalColour.BLUE.colour;
+    assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalBlue);
+
+    /*
+     * set directly to ignore gaps
+     */
+    cs.setIncludeGaps(false);
+    Color clustalPink = ClustalxColourScheme.ClustalColour.PINK.colour;
+    assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
+
+    /*
+     * set ignore gaps on the viewport...
+     */
+    cs.setIncludeGaps(true);
+    assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalBlue);
+    af.getViewport().setIgnoreGapsConsensus(true, af.alignPanel);
+    // next test fails: colour scheme does not read ignore gaps flag from
+    // viewport
+    // assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
+  }
 }