public class Utils
extends java.lang.Object
Constructor | Description |
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Utils() |
Modifier and Type | Method | Description |
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static java.lang.String |
checkSequence(java.lang.String sequence) |
Checks if the sequence contains invalid characters.
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static java.lang.String |
checkSequence(java.lang.String sequence,
java.util.Set<java.lang.Character> cSet) |
Checks if the sequence contains invalid characters.
|
static java.lang.String |
cleanSequence(java.lang.String sequence,
java.util.Set<java.lang.Character> cSet) |
Returns a new sequence with all invalid characters being replaced by '-'.
|
static boolean |
doesSequenceContainInvalidChar(java.lang.String sequence,
java.util.Set<java.lang.Character> cSet) |
Checks if given sequence contains invalid characters.
|
static int |
getNumberOfInvalidChar(java.lang.String sequence,
java.util.Set<java.lang.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.
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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(java.lang.String sequence, java.util.Set<java.lang.Character> cSet)
sequence
- protein sequence to be check.cSet
- the set of characters that are deemed valid.public static final int getNumberOfInvalidChar(java.lang.String sequence, java.util.Set<java.lang.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 ignoredpublic static final java.lang.String cleanSequence(java.lang.String sequence, java.util.Set<java.lang.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 java.lang.String checkSequence(java.lang.String sequence)
sequence
- protein sequence to be check for invalid characters.public static final java.lang.String checkSequence(java.lang.String sequence, java.util.Set<java.lang.Character> cSet)
sequence
- protein sequence to be check for invalid characters.cSet
- character set which define the valid characters.