X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FRnaTest.java;h=1faf3f2a85ff767931ed15526443a68728881e69;hb=1c52130ad032d77caac874c3a8be23a399a3ec93;hp=f96d2c909107545513af181578f408d6f668b40f;hpb=9c1dd670f293d8f33de55133397b4cd2d4baf38e;p=jalview.git

diff --git a/test/jalview/analysis/RnaTest.java b/test/jalview/analysis/RnaTest.java
index f96d2c9..1faf3f2 100644
--- a/test/jalview/analysis/RnaTest.java
+++ b/test/jalview/analysis/RnaTest.java
@@ -27,18 +27,29 @@ 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;
 
 public class RnaTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Functional" })
   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());
 
     /*
@@ -105,7 +116,7 @@ public class RnaTest
     {
       String s = String.valueOf((char) i);
       String ss = Rna.getRNASecStrucState(s);
-  
+
       /*
        * valid SS chars are a-z, A-Z, and various brackets;
        * anything else is returned as a space
@@ -120,7 +131,7 @@ public class RnaTest
         assertEquals(" ", ss);
       }
     }
-  
+
     /*
      * a string is processed character by character
      */
@@ -278,7 +289,7 @@ public class RnaTest
   public void testIsRnaSecondaryStructureSymbol()
   {
     assertFalse(Rna.isRnaSecondaryStructureSymbol(null));
-  
+
     /*
      * only A-Z,  a-z, ()[]{}<> are valid symbols
      */
@@ -303,4 +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());
+  }
 }