X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FRnaTest.java;h=f33525faf21a63e2198aafad82133fdc618f7e01;hb=2f497e35821e09179115565d29a26f41186385c7;hp=2c51a1ba01752ef157198c99461d661f53bcd934;hpb=0715e493687eeb93d3b3f39cd1ff25e2671ce0e9;p=jalview.git

diff --git a/test/jalview/analysis/RnaTest.java b/test/jalview/analysis/RnaTest.java
index 2c51a1b..f33525f 100644
--- a/test/jalview/analysis/RnaTest.java
+++ b/test/jalview/analysis/RnaTest.java
@@ -128,24 +128,34 @@ public class RnaTest
             Rna.getRNASecStrucState("a.[K-]z}?{Q b(w)p><i"));
   }
 
+  /**
+   * Tests for isClosingParenthesis with char or String argument
+   */
   @Test(groups = { "Functional" })
   public void testIsClosingParenthesis()
   {
+    assertFalse(Rna.isClosingParenthesis(null));
+
     /*
      * only a-z, )]}> are closing bracket symbols
      */
     for (int i = 0; i <= 255; i++)
     {
-      boolean isClosing = Rna.isClosingParenthesis((char) i);
+      boolean isClosingChar = Rna.isClosingParenthesis((char) i);
+      boolean isClosingString = Rna.isClosingParenthesis(String
+              .valueOf((char) i));
       if ((i >= 'a' && i <= 'z') || i == ')' || i == '}' || i == ']'
               || i == '>')
       {
-        assertTrue(String.format("close base pair %c", i), isClosing);
+        assertTrue(String.format("close base pair %c", i), isClosingChar);
+        assertTrue(String.format("close base pair %c", i), isClosingString);
       }
       else
       {
-        assertFalse(String.format("close base pair %c", i), isClosing);
+        assertFalse(String.format("close base pair %c", i), isClosingChar);
+        assertFalse(String.format("close base pair %c", i), isClosingString);
       }
+      assertFalse(Rna.isClosingParenthesis(String.valueOf((char) i) + " "));
     }
   }
 
@@ -178,6 +188,9 @@ public class RnaTest
     }
   }
 
+  /**
+   * Tests for isOpeningParenthesis with char or String argument
+   */
   @Test(groups = { "Functional" })
   public void testIsOpeningParenthesis()
   {
@@ -186,16 +199,81 @@ public class RnaTest
      */
     for (int i = 0; i <= 255; i++)
     {
-      boolean isOpening = Rna.isOpeningParenthesis((char) i);
+      boolean isOpeningChar = Rna.isOpeningParenthesis((char) i);
+      boolean isOpeningString = Rna.isOpeningParenthesis(String
+              .valueOf((char) i));
       if ((i >= 'A' && i <= 'Z') || i == '(' || i == '{' || i == '['
               || i == '<')
       {
-        assertTrue(String.format("Open base pair %c", i), isOpening);
+        assertTrue(String.format("Open base pair %c", i), isOpeningChar);
+        assertTrue(String.format("Open base pair %c", i), isOpeningString);
+      }
+      else
+      {
+        assertFalse(String.format("Open base pair %c", i), isOpeningChar);
+        assertFalse(String.format("Open base pair %c", i), isOpeningString);
+      }
+      assertFalse(Rna.isOpeningParenthesis(String.valueOf((char) i) + " "));
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetMatchingOpeningParenthesis() throws WUSSParseException
+  {
+    for (int i = 0; i <= 255; i++)
+    {
+      boolean isClosing = Rna.isClosingParenthesis((char) i);
+      if (isClosing)
+      {
+        char opening = Rna.getMatchingOpeningParenthesis((char) i);
+        if (i >= 'a' && i <= 'z')
+        {
+          assertEquals(i + 'A' - 'a', opening);
+        }
+        else if (i == ')' && opening == '(' || i == ']' && opening == '['
+                || i == '}' && opening == '{' || i == '>' && opening == '<')
+        {
+          // ok
+        }
+        else
+        {
+          fail("Got " + opening + " as opening bracket pair for "
+                  + ((char) i));
+        }
+      }
+    }
+  }
+
+  /**
+   * Tests for isRnaSecondaryStructureSymbol with char or String argument
+   */
+  @Test(groups = { "Functional" })
+  public void testIsRnaSecondaryStructureSymbol()
+  {
+    assertFalse(Rna.isRnaSecondaryStructureSymbol(null));
+  
+    /*
+     * only A-Z,  a-z, ()[]{}<> are valid symbols
+     */
+    for (int i = 0; i <= 255; i++)
+    {
+      boolean isValidChar = Rna.isRnaSecondaryStructureSymbol((char) i);
+      boolean isValidString = Rna.isRnaSecondaryStructureSymbol(String
+              .valueOf((char) i));
+      if ((i >= 'A' && i <= 'Z') || (i >= 'a' && i <= 'z') || i == '('
+              || i == ')' || i == '{' || i == '}' || i == '[' || i == ']'
+              || i == '<' || i == '>')
+      {
+        assertTrue(String.format("close base pair %c", i), isValidChar);
+        assertTrue(String.format("close base pair %c", i), isValidString);
       }
       else
       {
-        assertFalse(String.format("Open base pair %c", i), isOpening);
+        assertFalse(String.format("close base pair %c", i), isValidChar);
+        assertFalse(String.format("close base pair %c", i), isValidString);
       }
+      assertFalse(Rna.isRnaSecondaryStructureSymbol(String
+              .valueOf((char) i) + " "));
     }
   }
 }