*/
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;
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());
/*
{
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
assertEquals(" ", ss);
}
}
-
+
/*
* a string is processed character by character
*/
for (int i = 0; i <= 255; i++)
{
boolean isClosingChar = Rna.isClosingParenthesis((char) i);
- boolean isClosingString = Rna.isClosingParenthesis(String
- .valueOf((char) i));
+ boolean isClosingString = Rna
+ .isClosingParenthesis(String.valueOf((char) i));
if ((i >= 'a' && i <= 'z') || i == ')' || i == '}' || i == ']'
|| i == '>')
{
else
{
assertFalse(String.format("close base pair %c", i), isClosingChar);
- assertFalse(String.format("close base pair %c", i), isClosingString);
+ assertFalse(String.format("close base pair %c", i),
+ isClosingString);
}
assertFalse(Rna.isClosingParenthesis(String.valueOf((char) i) + " "));
}
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")
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"))
for (int i = 0; i <= 255; i++)
{
boolean isOpeningChar = Rna.isOpeningParenthesis((char) i);
- boolean isOpeningString = Rna.isOpeningParenthesis(String
- .valueOf((char) i));
+ boolean isOpeningString = Rna
+ .isOpeningParenthesis(String.valueOf((char) i));
if ((i >= 'A' && i <= 'Z') || i == '(' || i == '{' || i == '['
|| i == '<')
{
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));
+ 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 == '>')
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) + " "));
+ assertFalse(Rna.isRnaSecondaryStructureSymbol(
+ String.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());
+ }
}