public class Enzyme extends ExperimentObject
Constructor and Description |
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Enzyme(String name)
Constructor for an Enzyme.
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Modifier and Type | Method and Description |
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void |
addAminoAcidAfter(Character aminoAcid)
Adds an amino acid to the list of allowed amino acids after the cleavage
site.
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void |
addAminoAcidBefore(Character aminoAcid)
Adds an amino acid to the list of allowed amino acids before the cleavage
site.
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void |
addRestrictionAfter(Character aminoAcid)
Adds an amino acid to the list of forbidden amino acids after the
cleavage site.
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void |
addRestrictionBefore(Character aminoAcid)
Adds an amino acid to the list of forbidden amino acids before the
cleavage site.
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void |
backwardCompatibilityFix()
Converts a list based object (utilities older than 0.8.4) to a set based.
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HashSet<String> |
digest(String sequence,
int nMissedCleavages,
Double massMin,
Double massMax)
Digests a protein sequence in a list of expected peptide sequences.
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HashSet<String> |
digest(String sequence,
int nMissedCleavages,
Integer nMin,
Integer nMax)
Digests a protein sequence in a list of expected peptide sequences.
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boolean |
equals(Enzyme otherEnzyme)
Returns true of the two enzymes are identical.
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HashSet<Character> |
getAminoAcidAfter()
Getter for the amino acids potentially following the cleavage.
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HashSet<Character> |
getAminoAcidBefore()
Getter for the amino acids potentially preceding the cleavage.
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CvTerm |
getCvTerm()
Returns the CV term associated with this enzyme.
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String |
getDescription()
Returns the description of the cleavage of this enzyme.
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int |
getId()
Get the enzyme id.
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String |
getName()
Get the enzyme name.
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int |
getNmissedCleavages(String sequence)
Returns the number of missed cleavages in an amino acid sequence.
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HashSet<Character> |
getRestrictionAfter()
Getter for the amino acids restricting when following the cleavage.
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HashSet<Character> |
getRestrictionBefore()
Getter for the amino acids restricting when preceding the cleavage.
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boolean |
isCleavageSite(Character aaBefore,
Character aaAfter)
Returns a boolean indicating whether the given amino acids represent a
cleavage site.
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boolean |
isCleavageSite(String aaBefore,
String aaAfter)
Returns a boolean indicating whether the given amino acids represent a
cleavage site.
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boolean |
isCleavageSiteNoCombination(Character aaBefore,
Character aaAfter)
Returns a boolean indicating whether the given amino acids represent a
cleavage site.
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boolean |
isSemiSpecific()
Deprecated.
use the digestion preferences instead
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boolean |
isUnspecific()
Deprecated.
use the digestion preferences instead
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boolean |
isWholeProtein()
Deprecated.
use the digestion preferences instead
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void |
setCvTerm(CvTerm cvTerm)
Sets the CV term associated with this enzyme.
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addUrParam, clearParametersMap, getUrParam, removeUrParam
public Enzyme(String name)
name
- the name of the enzymepublic String getName()
public int getId()
public void backwardCompatibilityFix()
public void addAminoAcidAfter(Character aminoAcid)
aminoAcid
- an amino acid represented by its single amino acid code.public HashSet<Character> getAminoAcidAfter()
public void addAminoAcidBefore(Character aminoAcid)
aminoAcid
- an amino acid represented by its single amino acid code.public HashSet<Character> getAminoAcidBefore()
public void addRestrictionAfter(Character aminoAcid)
aminoAcid
- an amino acid represented by its single amino acid code.public HashSet<Character> getRestrictionAfter()
public void addRestrictionBefore(Character aminoAcid)
aminoAcid
- an amino acid represented by its single amino acid code.public HashSet<Character> getRestrictionBefore()
public boolean isCleavageSite(String aaBefore, String aaAfter)
aaBefore
- the amino acid before the cleavage siteaaAfter
- the amino acid after the cleavage sitepublic boolean isCleavageSite(Character aaBefore, Character aaAfter)
aaBefore
- the amino acid before the cleavage siteaaAfter
- the amino acid after the cleavage sitepublic boolean isCleavageSiteNoCombination(Character aaBefore, Character aaAfter)
aaBefore
- the amino acid before the cleavage siteaaAfter
- the amino acid after the cleavage sitepublic int getNmissedCleavages(String sequence)
sequence
- the amino acid sequence as a string.public HashSet<String> digest(String sequence, int nMissedCleavages, Integer nMin, Integer nMax)
sequence
- the protein sequencenMissedCleavages
- the maximum number of missed cleavagesnMin
- the minimal size for a peptide (inclusive, ignored if null)nMax
- the maximal size for a peptide (inclusive, ignored if null)public HashSet<String> digest(String sequence, int nMissedCleavages, Double massMin, Double massMax)
sequence
- the protein sequencenMissedCleavages
- the maximum number of missed cleavagesmassMin
- the minimal mass for a peptide (inclusive)massMax
- the maximal mass for a peptide (inclusive)public boolean equals(Enzyme otherEnzyme)
otherEnzyme
- the enzyme to compare against.public String getDescription()
public CvTerm getCvTerm()
public void setCvTerm(CvTerm cvTerm)
cvTerm
- the CV term associated with this enzymepublic boolean isUnspecific()
public boolean isSemiSpecific()
public boolean isWholeProtein()
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