public class RegExEnzyme extends Enzyme
C_TERM_ENZYMATIC, CTERM, ENTIRELY_NOT_ENZYMATIC, FULLY_ENZYMATIC, iCleavables, iCleavage, iMiscleavages, iPosition, iRestrict, iRestrictors, iTitle, N_TERM_ENZYMATIC, NTERM
Constructor and Description |
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RegExEnzyme(java.lang.String aTitle,
java.lang.String aCleavage,
java.lang.String aRestrict,
java.lang.String aPosition)
Create a new RegExEnzyme.
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RegExEnzyme(java.lang.String aTitle,
java.lang.String aCleavage,
java.lang.String aRestrict,
java.lang.String aPosition,
int aMiscleavages)
Create a new RegExEnzyme.
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Modifier and Type | Method and Description |
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Protein[] |
cleave(Protein aProtein)
This method is the focus of the Enzyme instance.
|
java.lang.Object |
clone()
This method returns a deep copy of the current Enzyme.
|
char[] |
getCleavage()
Simple getter for the cleavagable residus of the Enzyme.
|
int |
isEnzymaticProduct(java.lang.String aParentSequence,
int aStart,
int aEnd)
This method reports on the possibility that the presented subsequence
(represented by the start and end location in the parent) is the result
of enzymatic activity.
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int |
isEnzymaticProduct(java.lang.String aParentSequence,
java.lang.String aSubSequence)
This method reports on the possibility that the presented subsequence is
the result of enzymatic activity.
|
void |
setCleavage(char[] aCleavage)
This method allows the caller to specify the cleavable residus.
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void |
setCleavage(java.lang.String aCleavage)
This method can be used to set the cleavage pattern for this RegExEnzyme.
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java.lang.String |
toString()
This method generates a String representation of the Enzyme,
which is useful for displaying as useful information for the user or
during testing/debugging.
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java.lang.String |
toString(java.lang.String aPrepend)
This method generates a String representation of the Enzyme,
which is useful for displaying as useful information for the user or
during testing/debugging.
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cleave, getMiscleavages, getPosition, getRestrict, getTitle, setMiscleavages, setPosition, setRestrict, setRestrict, setTitle
public RegExEnzyme(java.lang.String aTitle, java.lang.String aCleavage, java.lang.String aRestrict, java.lang.String aPosition)
aTitle
- aCleavage
- aRestrict
- aPosition
- public RegExEnzyme(java.lang.String aTitle, java.lang.String aCleavage, java.lang.String aRestrict, java.lang.String aPosition, int aMiscleavages)
aTitle
- aCleavage
- aRestrict
- aPosition
- aMiscleavages
- public void setCleavage(java.lang.String aCleavage)
setCleavage
in class Enzyme
aCleavage
- a String representing the pattern for the cleavage site.java.util.regex.PatternSyntaxException
- if the provided string could not be compiled as regular expression.public void setCleavage(char[] aCleavage)
Enzyme
setCleavage
in class Enzyme
aCleavage
- char[] with the cleavable residus
(in UPPER CASE!).public char[] getCleavage()
Enzyme
getCleavage
in class Enzyme
public java.lang.String toString()
Enzyme
public java.lang.String toString(java.lang.String aPrepend)
Enzyme
public java.lang.Object clone()
Enzyme
public int isEnzymaticProduct(java.lang.String aParentSequence, java.lang.String aSubSequence)
Enzyme
isEnzymaticProduct
in class Enzyme
aParentSequence
- String with the parent sequenceaSubSequence
- String with the subsequencepublic int isEnzymaticProduct(java.lang.String aParentSequence, int aStart, int aEnd)
Enzyme
isEnzymaticProduct
in class Enzyme
aParentSequence
- String with the parent sequenceaStart
- int with the start of the subsequence relative to the parent (first residue is '1').aEnd
- int with the end of the subsequence relative to the parentpublic Protein[] cleave(Protein aProtein)
Enzyme
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