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java.lang.Objectcom.compomics.util.protein.Enzyme
com.compomics.util.protein.RegExEnzyme
public class RegExEnzyme
This class implements the functionality of an Enzyme by simulating digestion based on a regular expression.
Field Summary |
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Fields inherited from class com.compomics.util.protein.Enzyme |
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C_TERM_ENZYMATIC, CTERM, ENTIRELY_NOT_ENZYMATIC, FULLY_ENZYMATIC, iCleavables, iCleavage, iMiscleavages, iPosition, iRestrict, iRestrictors, iTitle, N_TERM_ENZYMATIC, NTERM |
Constructor Summary | |
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RegExEnzyme(String aTitle,
String aCleavage,
String aRestrict,
String aPosition)
Create a new RegExEnzyme. |
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RegExEnzyme(String aTitle,
String aCleavage,
String aRestrict,
String aPosition,
int aMiscleavages)
Create a new RegExEnzyme. |
Method Summary | |
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Protein[] |
cleave(Protein aProtein)
This method is the focus of the Enzyme instance. |
Object |
clone()
This method returns a deep copy of the current Enzyme. |
char[] |
getCleavage()
Simple getter for the cleavagable residues of the Enzyme. |
int |
isEnzymaticProduct(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. |
int |
isEnzymaticProduct(String aParentSequence,
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 residues. |
void |
setCleavage(String aCleavage)
This method can be used to set the cleavage pattern for this RegExEnzyme. |
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. |
String |
toString(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. |
Methods inherited from class com.compomics.util.protein.Enzyme |
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cleave, getMiscleavages, getPosition, getRestrict, getTitle, setMiscleavages, setPosition, setRestrict, setRestrict, setTitle |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public RegExEnzyme(String aTitle, String aCleavage, String aRestrict, String aPosition)
aTitle
- aCleavage
- aRestrict
- aPosition
- public RegExEnzyme(String aTitle, String aCleavage, String aRestrict, String aPosition, int aMiscleavages)
aTitle
- aCleavage
- aRestrict
- aPosition
- aMiscleavages
- Method Detail |
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public void setCleavage(String aCleavage)
setCleavage
in class Enzyme
aCleavage
- a String representing the pattern for the cleavage site.
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 residues (in UPPER
CASE!).public char[] getCleavage()
Enzyme
getCleavage
in class Enzyme
public String toString()
Enzyme
toString
in class Enzyme
public String toString(String aPrepend)
Enzyme
toString
in class Enzyme
aPrepend
- String to prepend to each outputted line.
public Object clone()
Enzyme
clone
in class Enzyme
public int isEnzymaticProduct(String aParentSequence, String aSubSequence)
Enzyme
isEnzymaticProduct
in class Enzyme
aParentSequence
- String with the parent sequenceaSubSequence
- String with the subsequence
public int isEnzymaticProduct(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 parent
public Protein[] cleave(Protein aProtein)
Enzyme
cleave
in class Enzyme
aProtein
- Protein instance to cleave.
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