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java.lang.Objectorg.biojava3.aaproperties.Utils
public class Utils
This is a utility class that contains utility methods which will facilitates the coding of other methods
Constructor Summary | |
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Utils()
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Method Summary | |
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static String |
checkSequence(String sequence)
Checks if the sequence contains invalid characters. |
static String |
checkSequence(String sequence,
Set<Character> cSet)
Checks if the sequence contains invalid characters. |
static String |
cleanSequence(String sequence,
Set<Character> cSet)
Returns a new sequence with all invalid characters being replaced by '-'. |
static boolean |
doesSequenceContainInvalidChar(String sequence,
Set<Character> cSet)
Checks if given sequence contains invalid characters. |
static int |
getNumberOfInvalidChar(String sequence,
Set<Character> cSet,
boolean ignoreCase)
Return the number of invalid characters in sequence. |
static double |
roundToDecimals(double d,
int c)
Returns a value with the desired number of decimal places. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Utils()
Method Detail |
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public static final double roundToDecimals(double d, int c)
d
- value to roundc
- number of decimal places desired.
Must be greater or equal to zero, otherwise, the given value d would be returned without any modification.
public static final boolean doesSequenceContainInvalidChar(String sequence, Set<Character> cSet)
sequence
- protein sequence to be check.cSet
- the set of characters that are deemed valid.
public static final int getNumberOfInvalidChar(String sequence, Set<Character> cSet, boolean ignoreCase)
sequence
- protein sequence to count for invalid characters.cSet
- the set of characters that are deemed valid.ignoreCase
- indicates if cases should be ignored
public static final String cleanSequence(String sequence, Set<Character> cSet)
sequence
- protein sequence to be cleancSet
- user defined characters that are valid. Can be null. If null, then 20 standard protein amino acid codes will be considered as valid.
public static final String checkSequence(String sequence)
sequence
- protein sequence to be check for invalid characters.
public static final String checkSequence(String sequence, Set<Character> cSet)
sequence
- protein sequence to be check for invalid characters.cSet
- character set which define the valid characters.
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