Merge remote-tracking branch 'origin/bug/JAL-3141_Messages_discrepancy_fix' into...

[jalview.git] / test / jalview / analysis / AlignSeqTest.java

diff --git a/test/jalview/analysis/AlignSeqTest.java b/test/jalview/analysis/AlignSeqTest.java
index 34ae612..bd827f9 100644 (file)
--- a/test/jalview/analysis/AlignSeqTest.java
+++ b/test/jalview/analysis/AlignSeqTest.java
@@ -1,23 +1,79 @@
+/*
+ * 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.analysis;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
+import jalview.datamodel.Sequence;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class AlignSeqTest
 {
-  @Test(groups ={ "Functional" })
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = { "Functional" })
   public void testExtractGaps()
   {
     assertNull(AlignSeq.extractGaps(null, null));
     assertNull(AlignSeq.extractGaps(null, "ACG"));
     assertNull(AlignSeq.extractGaps("-. ", null));
 
-    assertEquals(" AC-G.T", AlignSeq.extractGaps("", " AC-G.T"));
-    assertEquals("AC-G.T", AlignSeq.extractGaps(" ", " AC-G.T"));
-    assertEquals("ACG.T", AlignSeq.extractGaps(" -", " AC-G.T"));
-    assertEquals("ACGT", AlignSeq.extractGaps(" -.", " AC-G.T ."));
-    assertEquals(" ACG.T", AlignSeq.extractGaps("-", " AC-G.T"));
+    assertEquals(AlignSeq.extractGaps("", " AC-G.T"), " AC-G.T");
+    assertEquals(AlignSeq.extractGaps(" ", " AC-G.T"), "AC-G.T");
+    assertEquals(AlignSeq.extractGaps(" -", " AC-G.T"), "ACG.T");
+    assertEquals(AlignSeq.extractGaps(" -.", " AC-G.T ."), "ACGT");
+    assertEquals(AlignSeq.extractGaps("-", " AC-G.T"), " ACG.T");
+    assertEquals(AlignSeq.extractGaps("-. ", " -. .-"), "");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIndexEncode_nucleotide()
+  {
+    AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"), new Sequence(
+            "s2", "ACGT"), AlignSeq.DNA);
+    int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6,
+        7, 7, 8, 8, 9, 9, -1, -1, 10, -1 };
+    String s = "aAcCgGtTuUiIxXrRyYnN .-?";
+    assertArrayEquals(expected, as.indexEncode(s));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIndexEncode_peptide()
+  {
+    AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"), new Sequence(
+            "s2", "RQW"), AlignSeq.PEP);
+    int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, -1, 23,
+        -1, -1, -1 };
+    String s = "aArRnNzZxX *.-?";
+    assertArrayEquals(expected, as.indexEncode(s));
   }
 }