*/
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;
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 == '<')
{
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) + " "));
}
}
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)