Enzyme (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.protein.Enzyme

All Implemented Interfaces:

Cloneable

Direct Known Subclasses:

DualEnzyme, RegExEnzyme
```
public class Enzyme
extends Object
implements Cloneable
```
This class implements the functionality for an Enzyme.

Author:

Lennart Martens, Harald Barsnes

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`C_TERM_ENZYMATIC`
`static int`	`CTERM`
`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

Constructors
Constructor and Description
`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.
`Enzyme(String aTitle, String aCleavage, String aRestrict, String aPosition)` This constructor requires that you specify all the information for this enzyme.
`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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`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
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - CTERM
```
public static final int CTERM
```
    See Also:
    
    Constant Field Values
  - NTERM
```
public static final int NTERM
```
    See Also:
    
    Constant Field Values
  - FULLY_ENZYMATIC
```
public static final int FULLY_ENZYMATIC
```
    See Also:
    
    Constant Field Values
  - N_TERM_ENZYMATIC
```
public static final int N_TERM_ENZYMATIC
```
    See Also:
    
    Constant Field Values
  - C_TERM_ENZYMATIC
```
public static final int C_TERM_ENZYMATIC
```
    See Also:
    
    Constant Field Values
  - ENTIRELY_NOT_ENZYMATIC
```
public static final int ENTIRELY_NOT_ENZYMATIC
```
    See Also:
    
    Constant Field Values
  - iTitle
```
protected String iTitle
```
    This String holds the title (or name) for the enzyme.
  - iCleavage
```
protected char[] iCleavage
```
    This char[] holds the residues after which cleavage will occur.
  - iCleavables
```
protected HashMap iCleavables
```
    Lookup cache for the cleavable residues.
  - iRestrict
```
protected char[] iRestrict
```
    This char[] holds the residues that will restrict cleavage when present after a cleavable residue.
  - iRestrictors
```
protected HashMap iRestrictors
```
    Lookup cache for the restricting residues.
  - iPosition
```
protected int iPosition
```
    This integer holds the position marker for the cleavage direction for this Enzyme. This variable can be matched against the constants defined on this class.
  - iMiscleavages
```
protected int iMiscleavages
```
    This variable holds the number of supported missed cleavages.
- Constructor Detail
  - Enzyme
```
public Enzyme(String aTitle,
              String aCleavage,
              String aRestrict,
              String aPosition)
```
    This constructor requires that you specify all the information for this enzyme. Title and restrict can be 'null', and the number of miscleavages is defaulted to 1.
    
    Parameters:
    
    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.
  - Enzyme
```
public 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. Title and restrict can be 'null'.
    
    Parameters:
    
    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.
  - Enzyme
```
public 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. We put a lot of efforts in standardizing all objects into the experiment package. We are now very happy to provide you the opportunity to mess up your code!
    
    Parameters:
    
    enzyme - The com.compomics.util.experiment.biology.Enzyme enzyme
    
    maxMissedCleavages - The maximum number of missed cleavages
- Method Detail
  - getTitle
```
public String getTitle()
```
    Simple getter for the title (name) of the Enzyme.
    
    Returns:
    
    String with the title (name).
  - setTitle
```
public void setTitle(String aTitle)
```
    This method allows the caller to change the title (name) of the Enzyme.
    
    Parameters:
    
    aTitle - String with the title (name) for the Enzyme.
  - getCleavage
```
public char[] getCleavage()
```
    Simple getter for the cleavagable residues of the Enzyme.
    
    Returns:
    
    char[] with the cleavable residues.
  - setCleavage
```
public void setCleavage(char[] aCleavage)
```
    This method allows the caller to specify the cleavable residues.
    
    Parameters:
    
    aCleavage - char[] with the cleavable residues (in UPPER CASE!).
  - setCleavage
```
public void setCleavage(String aCleavage)
```
    This method allows the caller to specify the cleavable residues. They will be read from the String as a continuous summation of characters (i.e: 'RKGH').
    
    Parameters:
    
    aCleavage - String with the continuous characters corresponding to the cleavable residues. Note that the String is uppercased.
  - getRestrict
```
public char[] getRestrict()
```
    Simple getter for the restricting residues of the Enzyme.
    
    Returns:
    
    char[] with the restricting residues.
  - setRestrict
```
public void setRestrict(char[] aRestrict)
```
    This method allows the caller to specify the residues that restrict cleavage.
    
    Parameters:
    
    aRestrict - char[] with the residues (in UPPER CASE!) which restrict cleavage.
  - setRestrict
```
public void setRestrict(String aRestrict)
```
    This method allows the caller to specify the residues which restrict cleavage. They will be read from the String as a continuous summation of characters (i.e: 'PGHK').
    
    Parameters:
    
    aRestrict - String with the continuous characters corresponding to the restricting residues. Note that the String is uppercased.
  - getPosition
```
public int getPosition()
```
    Simple getter for the cleavage position of the Enzyme.
    
    Returns:
    
    int with the coded cleavage position (to be compared with the constants on this class).
  - setPosition
```
public void setPosition(int aPosition)
```
    This method allows the caller to set the cleavage position for the Enzyme. Please use the constants defined on this class as parameters.
    
    Parameters:
    
    aPosition - int with the coded position, according to the constants on this class.
  - getMiscleavages
```
public int getMiscleavages()
```
    Simple getter for the number of allowed missed cleavages for the Enzyme.
    
    Returns:
    
    int with the number of allowed missed cleavages.
  - setMiscleavages
```
public void setMiscleavages(int aMiscleavages)
```
    This method allows the caller to specify the number of allowed missed cleavages for this enzyme.
    
    Parameters:
    
    aMiscleavages - int with the number of allowed missed cleavages.
  - toString
```
public 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.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    
    String with a textual description of this Enzyme.
  - toString
```
public 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. It takes a parameter String that is prepended to each line.
    
    Parameters:
    
    aPrepend - String to prepend to each outputted line.
    
    Returns:
    
    String with a textual description of this Enzyme.
  - cleave
```
public Protein[] cleave(Protein aProtein)
```
    This method is the focus of the Enzyme instance. It can perform an in-silico digest of a Protein sequence according to the specifications detailed in the construction or via the setters. Using this methods returns all possible peptides, regardless of length. To only return peptides within certain lengths use the other cleave method.
    
    Parameters:
    
    aProtein - Protein instance to cleave.
    
    Returns:
    
    Protein[] with the resultant peptides.
  - cleave
```
public Protein[] cleave(Protein aProtein,
                        int minPeptideLength,
                        int maxPeptideLength)
```
    This method is the focus of the Enzyme instance. It can perform an in-silico digest of a Protein sequence according to the specifications detailed in the construction or via the setters. Only returns peptides between the minimum and maximum peptide lengths.
    
    Parameters:
    
    aProtein - Protein instance to cleave.
    
    minPeptideLength - The minimum peptide length to consider
    
    maxPeptideLength - The maximum peptide length to consider
    
    Returns:
    
    Protein[] with the resultant peptides.
  - clone
```
public Object clone()
```
    This method returns a deep copy of the current Enzyme.
    
    Overrides:
    
    clone in class Object
    
    Returns:
    
    Object Enzyme instance that is a deep copy of the current Enzyme.
  - isEnzymaticProduct
```
public int isEnzymaticProduct(String aParentSequence,
                              String aSubSequence)
```
    This method reports on the possibility that the presented subsequence is the result of enzymatic activity. Note that using a substring, only the FIRST (starting from the N-terminus) occurrence of the subsequence in the parent String will be considered! If multiple occurrences are possible, use the overloaded method that takes indices. Returning int values can be checked against public static final vars on this class.
    
    Parameters:
    
    aParentSequence - String with the parent sequence
    
    aSubSequence - String with the subsequence
    
    Returns:
    
    int with the coded possibility (1 = Full enzymatic product, 2 = N-terminal half enzymatic product, 3 = C-terminal half enzymatic product and 4 = Entirely not an enzymatic product.
  - isEnzymaticProduct
```
public 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. Returning int values can be checked against public static final vars on this class.
    
    Parameters:
    
    aParentSequence - String with the parent sequence
    
    aStart - 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
    
    Returns:
    
    int with the coded possibility (1 = Full enzymatic product, 2 = N-terminal half enzymatic product, 3 = C-terminal half enzymatic product and 4 = Entirely not an enzymatic product.

Class Enzyme

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

CTERM

NTERM

FULLY_ENZYMATIC

N_TERM_ENZYMATIC

C_TERM_ENZYMATIC

ENTIRELY_NOT_ENZYMATIC

iTitle

iCleavage

iCleavables

iRestrict

iRestrictors

iPosition

iMiscleavages

Constructor Detail

Enzyme

Enzyme

Enzyme

Method Detail

getTitle

setTitle

getCleavage

setCleavage

setCleavage

getRestrict

setRestrict

setRestrict

getPosition

setPosition

getMiscleavages

setMiscleavages

toString

toString

cleave

cleave

clone

isEnzymaticProduct

isEnzymaticProduct