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java.lang.Objectcom.compomics.util.protein.Enzyme
public class Enzyme
This class implements the functionality for an Enzyme.
Field Summary | |
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static int |
C_TERM_ENZYMATIC
|
static int |
CTERM
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static int |
ENTIRELY_NOT_ENZYMATIC
|
static int |
FULLY_ENZYMATIC
|
protected HashMap |
iCleavables
Lookup cache for the cleavable residues. |
protected char[] |
iCleavage
This char[] holds the residues after which cleavage will occur. |
protected int |
iMiscleavages
This variable holds the number of supported missed cleavages. |
protected int |
iPosition
This integer holds the position marker for the cleavage direction for this Enzyme. |
protected char[] |
iRestrict
This char[] holds the residues that will restrict cleavage when present after a cleavable residue. |
protected HashMap |
iRestrictors
Lookup cache for the restricting residues. |
protected String |
iTitle
This String holds the title (or name) for the enzyme. |
static int |
N_TERM_ENZYMATIC
|
static int |
NTERM
|
Constructor Summary | |
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Enzyme(Enzyme enzyme,
int maxMissedCleavages)
Creates a new Enzyme from a com.compomics.util.experiment.biology.Enzyme enzyme and the maximum number of missed cleavages. |
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Enzyme(String aTitle,
String aCleavage,
String aRestrict,
String aPosition)
This constructor requires that you specify all the information for this enzyme. |
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Enzyme(String aTitle,
String aCleavage,
String aRestrict,
String aPosition,
int aMiscleavages)
This constructor allows you to specify all the information for this enzyme plus the number of missed cleavages that this instance will allow. |
Method Summary | |
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Protein[] |
cleave(Protein aProtein)
This method is the focus of the Enzyme instance. |
Protein[] |
cleave(Protein aProtein,
int minPeptideLength,
int maxPeptideLength)
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 |
getMiscleavages()
Simple getter for the number of allowed missed cleavages for the Enzyme. |
int |
getPosition()
Simple getter for the cleavage position of the Enzyme. |
char[] |
getRestrict()
Simple getter for the restricting residues of the Enzyme. |
String |
getTitle()
Simple getter for the title (name) 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 allows the caller to specify the cleavable residues. |
void |
setMiscleavages(int aMiscleavages)
This method allows the caller to specify the number of allowed missed cleavages for this enzyme. |
void |
setPosition(int aPosition)
This method allows the caller to set the cleavage position for the Enzyme. |
void |
setRestrict(char[] aRestrict)
This method allows the caller to specify the residues that restrict cleavage. |
void |
setRestrict(String aRestrict)
This method allows the caller to specify the residues which restrict cleavage. |
void |
setTitle(String aTitle)
This method allows the caller to change the title (name) of the Enzyme. |
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 java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final int CTERM
public static final int NTERM
public static final int FULLY_ENZYMATIC
public static final int N_TERM_ENZYMATIC
public static final int C_TERM_ENZYMATIC
public static final int ENTIRELY_NOT_ENZYMATIC
protected String iTitle
protected char[] iCleavage
protected HashMap iCleavables
protected char[] iRestrict
protected HashMap iRestrictors
protected int iPosition
protected int iMiscleavages
Constructor Detail |
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public Enzyme(String aTitle, String aCleavage, String aRestrict, String aPosition)
aTitle
- String with the title (or name) for this enzyme.aCleavage
- String composed of the residues after which cleavage
will occur.aRestrict
- String composed of the residues which inhibit cleavage
if present behind of cleavable residues.aPosition
- String which should correspond to "Cterm" or "Nterm" for
each position respectively.public Enzyme(String aTitle, String aCleavage, String aRestrict, String aPosition, int aMiscleavages)
aTitle
- String with the title (or name) for this enzyme.aCleavage
- String composed of the residues after which cleavage
will occur (this String will be uppercased).aRestrict
- String composed of the residues which inhibit cleavage if
present behind of cleavable residues (this String will be uppercased).aPosition
- String which should correspond to "Cterm" or "Nterm" for
each position respectively.aMiscleavages
- integer with the number of supported missed cleavages.public Enzyme(Enzyme enzyme, int maxMissedCleavages)
enzyme
- The com.compomics.util.experiment.biology.Enzyme enzymemaxMissedCleavages
- The maximum number of missed cleavagesMethod Detail |
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public String getTitle()
public void setTitle(String aTitle)
aTitle
- String with the title (name) for the Enzyme.public char[] getCleavage()
public void setCleavage(char[] aCleavage)
aCleavage
- char[] with the cleavable residues (in UPPER
CASE!).public void setCleavage(String aCleavage)
aCleavage
- String with the continuous characters corresponding to
the cleavable residues. Note that the String is uppercased.public char[] getRestrict()
public void setRestrict(char[] aRestrict)
aRestrict
- char[] with the residues (in UPPER CASE!) which
restrict cleavage.public void setRestrict(String aRestrict)
aRestrict
- String with the continuous characters corresponding to
the restricting residues. Note that the String is uppercased.public int getPosition()
public void setPosition(int aPosition)
aPosition
- int with the coded position, according to the constants
on this class.public int getMiscleavages()
public void setMiscleavages(int aMiscleavages)
aMiscleavages
- int with the number of allowed missed cleavages.public String toString()
toString
in class Object
public String toString(String aPrepend)
aPrepend
- String to prepend to each outputted line.
public Protein[] cleave(Protein aProtein)
aProtein
- Protein instance to cleave.
public Protein[] cleave(Protein aProtein, int minPeptideLength, int maxPeptideLength)
aProtein
- Protein instance to cleave.minPeptideLength
- The minimum peptide length to considermaxPeptideLength
- The maximum peptide length to consider
public Object clone()
clone
in class Object
public int isEnzymaticProduct(String aParentSequence, String aSubSequence)
aParentSequence
- String with the parent sequenceaSubSequence
- String with the subsequence
public int isEnzymaticProduct(String aParentSequence, int aStart, int aEnd)
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
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