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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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 |
getEnzymeId()
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(char aaBefore,
char 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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void |
setCvTerm(CvTerm cvTerm)
Sets the CV term associated with this enzyme.
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addUrParam, asLong, clearParametersMap, getUrParam, getUrParams, removeUrParam, setUrParams
getFirstLevel, getId, setFirstLevel, setId
jdoZooEvict, jdoZooGetBackup, jdoZooGetClassDef, jdoZooGetContext, jdoZooGetNode, jdoZooGetOid, jdoZooGetTimestamp, jdoZooHasState, jdoZooInit, jdoZooIsDeleted, jdoZooIsDetached, jdoZooIsDirty, jdoZooIsNew, jdoZooIsPersistent, jdoZooIsStateHollow, jdoZooIsTransactional, jdoZooMarkClean, jdoZooMarkDeleted, jdoZooMarkDetached, jdoZooMarkDirty, jdoZooMarkHollow, jdoZooMarkTransient, jdoZooSetOid, jdoZooSetTimestamp, toString, zooActivateRead, zooActivateWrite, zooActivateWrite
public Enzyme(String name)
name
- the name of the enzymepublic String getName()
public int getEnzymeId()
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(char aaBefore, char 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 enzymeCopyright © 2018. All rights reserved.