X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FRnaTest.java;h=cc35976ba18ffef4a0d0030997da5e4ec5bd31e2;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=9d35a1929d64fa2ac031f3fc96dd411e966a63a5;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/test/jalview/analysis/RnaTest.java b/test/jalview/analysis/RnaTest.java
index 9d35a19..cc35976 100644
--- a/test/jalview/analysis/RnaTest.java
+++ b/test/jalview/analysis/RnaTest.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import java.util.Locale;
+
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
@@ -27,18 +29,29 @@ 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());
 
     /*
@@ -171,7 +184,7 @@ public class RnaTest
         char second = bases.charAt(j);
         boolean result = Rna.isCanonicalOrWobblePair(first, second);
         String pair = new String(new char[] { first, second })
-                .toUpperCase();
+                .toUpperCase(Locale.ROOT);
         if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
                 || pair.equals("UA") || pair.equals("GC")
                 || pair.equals("CG") || pair.equals("GT")
@@ -200,7 +213,7 @@ public class RnaTest
         char second = bases.charAt(j);
         boolean result = Rna.isCanonicalPair(first, second);
         String pair = new String(new char[] { first, second })
-                .toUpperCase();
+                .toUpperCase(Locale.ROOT);
         if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
                 || pair.equals("UA") || pair.equals("GC")
                 || pair.equals("CG"))
@@ -303,4 +316,54 @@ 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());
+  }
 }