JAL-2446 merged to spike branch

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

diff --git a/test/jalview/analysis/RnaTest.java b/test/jalview/analysis/RnaTest.java
index 814d2d4..1faf3f2 100644 (file)
--- a/test/jalview/analysis/RnaTest.java
+++ b/test/jalview/analysis/RnaTest.java
@@ -27,9 +27,10 @@ import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 
 import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.datamodel.SequenceFeature;
 import jalview.gui.JvOptionPane;
 
-import java.util.Vector;
+import java.util.List;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -48,7 +49,7 @@ public class RnaTest
   public void testGetSimpleBPs() throws WUSSParseException
   {
     String rna = "([{})]"; // JAL-1081 example
-    Vector<SimpleBP> bps = Rna.getSimpleBPs(rna);
+    List<SimpleBP> bps = Rna.getSimpleBPs(rna);
     assertEquals(3, bps.size());
 
     /*
@@ -313,4 +314,54 @@ public class RnaTest
               .valueOf((char) i) + " "));
     }
   }
+
+  @Test(groups = "Functional")
+  public void testGetHelixMap_oneHelix() throws WUSSParseException
+  {
+    String rna = ".(..[{.<..>}..].)";
+    SequenceFeature[] sfs = Rna.getHelixMap(rna);
+    assertEquals(4, sfs.length);
+
+    /*
+     * pairs are added in the order in which the closing bracket is found
+     * (see testGetSimpleBPs)
+     */
+    assertEquals(7, sfs[0].getBegin());
+    assertEquals(10, sfs[0].getEnd());
+    assertEquals("0", sfs[0].getFeatureGroup());
+    assertEquals(5, sfs[1].getBegin());
+    assertEquals(11, sfs[1].getEnd());
+    assertEquals("0", sfs[1].getFeatureGroup());
+    assertEquals(4, sfs[2].getBegin());
+    assertEquals(14, sfs[2].getEnd());
+    assertEquals("0", sfs[2].getFeatureGroup());
+    assertEquals(1, sfs[3].getBegin());
+    assertEquals(16, sfs[3].getEnd());
+    assertEquals("0", sfs[3].getFeatureGroup());
+  }
+
+  @Test(groups = "Functional")
+  public void testGetHelixMap_twoHelices() throws WUSSParseException
+  {
+    String rna = ".([.)]..{.<}.>";
+    SequenceFeature[] sfs = Rna.getHelixMap(rna);
+    assertEquals(4, sfs.length);
+  
+    /*
+     * pairs are added in the order in which the closing bracket is found
+     * (see testGetSimpleBPs)
+     */
+    assertEquals(1, sfs[0].getBegin());
+    assertEquals(4, sfs[0].getEnd());
+    assertEquals("0", sfs[0].getFeatureGroup());
+    assertEquals(2, sfs[1].getBegin());
+    assertEquals(5, sfs[1].getEnd());
+    assertEquals("0", sfs[1].getFeatureGroup());
+    assertEquals(8, sfs[2].getBegin());
+    assertEquals(11, sfs[2].getEnd());
+    assertEquals("1", sfs[2].getFeatureGroup());
+    assertEquals(10, sfs[3].getBegin());
+    assertEquals(13, sfs[3].getEnd());
+    assertEquals("1", sfs[3].getFeatureGroup());
+  }
 }