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java.lang.Objectcom.compomics.util.protein.Enzyme
com.compomics.util.protein.DualEnzyme
public class DualEnzyme
This class implements an enzyme with a dual specificity; the N-terminus of a resultant peptide will have certain residue, the C-terminus will have another, eg. for a C-terminal cutter with N-terminal specificty for 'D' and C-terminal specificity for 'R': (D)XXXXXR; for an N-terminal cutter with N-terminal specificty for 'W' and C-terminal specificity for 'K': WXXXXX(K).
Field Summary | |
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static int |
CTERMINAL
The code for C-terminal position in the resultant peptide. |
static int |
NTERMINAL
The code for N-terminal position in the resultant peptide. |
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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DualEnzyme(String aTitle,
String aNtermCleavage,
String aCtermCleavage,
String aRestrict,
String aPosition)
This constructor allows you to specify all the information for this enzyme. |
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DualEnzyme(String aTitle,
String aNtermCleavage,
String aCtermCleavage,
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. |
Object |
clone()
Provides a cloned version of this DualEnzyme. |
char[] |
getCleavage()
Simple getter for the cleavable residues of the Enzyme. |
char[] |
getCleavage(int aTerminus)
This method returns the residues that are used for cleavage at the respective locations. |
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. |
static void |
main(String[] args)
Tests the DualEnzyme by digesting a hardcoded protein. |
Protein[] |
oldCleave(Protein aProtein)
This cleave method will process sequence XDYRZ solely into YR peptides. |
void |
setCleavage(char[] aCleavage)
This method allows the caller to specify the cleavable residues. |
void |
setCleavage(char[] aCleavage,
int aTerminus)
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 |
setCleavage(String aCleavage,
int aTerminus)
This method allows the caller to specify the cleavable residus. |
String |
toString()
This method generates a String representation of the DualEnzyme, 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 DualEnzyme, 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, isEnzymaticProduct, 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 |
Field Detail |
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public static final int NTERMINAL
public static final int CTERMINAL
Constructor Detail |
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public DualEnzyme(String aTitle, String aNtermCleavage, String aCtermCleavage, String aRestrict, String aPosition, int aMiscleavages)
aTitle
- String with the title (or name) for this enzyme.aNtermCleavage
- String composed of the residues after which cleavage
will occur at the N-terminus of the resultant peptide
(this String will be uppercased).aCtermCleavage
- String composed of the residues after which cleavage
will occur at the C-terminus of the resultant peptide
(this String will be uppercased).aRestrict
- String composed of the residues which inhibit cleavage
if present behind any of the cleavable residues (this String will be uppercased).aPosition
- String which should correspond to "Cterm" or "Nterm"
for each position respectively.aMiscleavages
- int with the number of supported missed cleavages.public DualEnzyme(String aTitle, String aNtermCleavage, String aCtermCleavage, String aRestrict, String aPosition)
aTitle
- String with the title (or name) for this enzyme.aNtermCleavage
- String composed of the residues after which cleavage
will occur at the N-terminus of the resultant peptide
(this String will be uppercased).aCtermCleavage
- String composed of the residues after which cleavage
will occur at the C-terminus of the resultant peptide
(this String will be uppercased).aRestrict
- String composed of the residues which inhibit cleavage
if present behind any of the cleavable residues (this String will be uppercased).aPosition
- String which should correspond to "Cterm" or "Nterm"
for each position respectively.Method Detail |
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public void setCleavage(char[] aCleavage)
setCleavage
in class Enzyme
aCleavage
- char[] with the cleavable residues
(in UPPER CASE!).public void setCleavage(String aCleavage)
setCleavage
in class Enzyme
aCleavage
- String with the continuous characters
corresponding to the cleavable residues.
Note that the String is uppercased.public void setCleavage(char[] aCleavage, int aTerminus)
aCleavage
- char[] with the cleavable residues
(in UPPER CASE!).aTerminus
- int with the code for the terminal position in
the resultant peptide. Can be 'NTERMINAL' or 'CTERMINAL'.public void setCleavage(String aCleavage, int aTerminus)
aCleavage
- String with the continuous characters
corresponding to the cleavable residues.
Note that the String is uppercased.aTerminus
- int with the code for the terminal position in
the resultant peptide. Can be 'NTERMINAL' or 'CTERMINAL'.public char[] getCleavage(int aTerminus)
aTerminus
- int with the code for the terminal position in
the resultant peptide. Can be 'NTERMINAL' or 'CTERMINAL'.
public char[] getCleavage()
getCleavage
in class Enzyme
public Object clone()
clone
in class Enzyme
public String toString()
toString
in class Enzyme
public String toString(String aPrepend)
toString
in class Enzyme
aPrepend
- String to prepend to each outputted line.
public Protein[] oldCleave(Protein aProtein)
aProtein
- Protein instance to cleave.
public Protein[] cleave(Protein aProtein)
cleave
in class Enzyme
aProtein
- Protein instance to cleave.
public int isEnzymaticProduct(String aParentSequence, int aStart, int aEnd)
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 static void main(String[] args)
args
-
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