Class PeptideDraft
java.lang.Object
com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
public class PeptideDraft extends Object
Draft of a peptide used during protein sequence digestion.
- Author:
- Marc Vaudel
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Constructor Summary
Constructors Constructor Description PeptideDraft()
Empty default constructorPeptideDraft(char[] sequence)
Constructor.PeptideDraft(char[] sequence, String nTermModification, String cTermModification, HashMap<Integer,String> fixedAaModifications, double mass)
Constructor.PeptideDraft(char[] sequence, String nTermModification, String cTermModification, HashMap<Integer,String> fixedAaModifications, double mass, int missedCleavages)
Constructor.PeptideDraft(char[] sequence, String nTermModification, HashMap<Integer,String> fixedAaModifications, double mass)
Constructor.PeptideDraft(char[] sequence, String nTermModification, HashMap<Integer,String> fixedAaModifications, double mass, int missedCleavages)
Constructor. -
Method Summary
Modifier and Type Method Description PeptideDraft
clone()
Creates a new peptide draft with the same attributes as this one.String
getcTermModification()
Returns the C-term modification.HashMap<Integer,String>
getFixedAaModifications()
Returns the modifications at specific amino acids.String[]
getFixedModifications()
Returns the fixed modifications for the peptide.int
getIndexOnProtein()
Returns the peptide index on the protein.double
getMass()
Returns the mass.int
getMissedCleavages()
Returns the number of missed cleavages.String
getnTermModification()
Returns the N-term modification.int
getnX()
Returns the number of Xs already considered in this draft.ExtendedPeptide
getPeptide(double massMin, double massMax)
Returns a peptide from the peptide draft.ExtendedPeptide
getPeptide(double massMin, double massMax, BoxedObject<Boolean> smallMass)
Returns a peptide from the peptide draft.char[]
getSequence()
Returns the sequence.void
increaseMissedCleavages()
Increases the number of missed cleavages.void
increaseNX()
Increases the number of Xs already considered in this draft.int
length()
Returns the length of the sequence.void
setcTermModification(String cTermModification)
Sets the C-term modification.void
setFixedAaModifications(HashMap<Integer,String> fixedAaModifications)
Sets the modifications at specific amino acids.void
setIndexOnProtein(int indexOnProtein)
Sets the peptide index on the protein.void
setMass(double mass)
Sets the mass.void
setnTermModification(String nTermModification)
Sets the N-term modification.void
setSequence(char[] sequence)
Sets the sequence.
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Constructor Details
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PeptideDraft
public PeptideDraft()Empty default constructor -
PeptideDraft
public PeptideDraft(char[] sequence)Constructor.- Parameters:
sequence
- the peptide sequence.
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PeptideDraft
public PeptideDraft(char[] sequence, String nTermModification, HashMap<Integer,String> fixedAaModifications, double mass)Constructor.- Parameters:
sequence
- the peptide sequencenTermModification
- the N-term modificationfixedAaModifications
- the fixed modifications at amino acidsmass
- the mass
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PeptideDraft
public PeptideDraft(char[] sequence, String nTermModification, HashMap<Integer,String> fixedAaModifications, double mass, int missedCleavages)Constructor.- Parameters:
sequence
- the peptide sequencenTermModification
- the N-term modificationfixedAaModifications
- the fixed modifications at amino acidsmass
- the massmissedCleavages
- the number of missed cleavages
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PeptideDraft
public PeptideDraft(char[] sequence, String nTermModification, String cTermModification, HashMap<Integer,String> fixedAaModifications, double mass)Constructor.- Parameters:
sequence
- the peptide sequencenTermModification
- the N-term modificationcTermModification
- the C-term modificationfixedAaModifications
- the fixed modifications at amino acidsmass
- the mass
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PeptideDraft
public PeptideDraft(char[] sequence, String nTermModification, String cTermModification, HashMap<Integer,String> fixedAaModifications, double mass, int missedCleavages)Constructor.- Parameters:
sequence
- the peptide sequencenTermModification
- the N-term modificationcTermModification
- the C-term modificationfixedAaModifications
- the fixed modifications at amino acidsmass
- the massmissedCleavages
- the number of missed cleavages
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Method Details
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clone
Creates a new peptide draft with the same attributes as this one. -
getSequence
public char[] getSequence()Returns the sequence.- Returns:
- the sequence
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setSequence
public void setSequence(char[] sequence)Sets the sequence.- Parameters:
sequence
- the sequence
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length
public int length()Returns the length of the sequence.- Returns:
- the length of the sequence
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getnTermModification
Returns the N-term modification.- Returns:
- the N-term modification
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setnTermModification
Sets the N-term modification.- Parameters:
nTermModification
- the N-term modification
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getcTermModification
Returns the C-term modification.- Returns:
- the C-term modification
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setcTermModification
Sets the C-term modification.- Parameters:
cTermModification
- the C-term modification
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getMass
public double getMass()Returns the mass.- Returns:
- the mass
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setMass
public void setMass(double mass)Sets the mass.- Parameters:
mass
- the mass
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getFixedAaModifications
Returns the modifications at specific amino acids.- Returns:
- the modifications at specific amino acids
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setFixedAaModifications
Sets the modifications at specific amino acids.- Parameters:
fixedAaModifications
- the modifications at specific amino acids
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increaseMissedCleavages
public void increaseMissedCleavages()Increases the number of missed cleavages. -
getMissedCleavages
public int getMissedCleavages()Returns the number of missed cleavages.- Returns:
- the number of missed cleavages
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increaseNX
public void increaseNX()Increases the number of Xs already considered in this draft. -
getnX
public int getnX()Returns the number of Xs already considered in this draft.- Returns:
- the number of Xs
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getIndexOnProtein
public int getIndexOnProtein()Returns the peptide index on the protein.- Returns:
- the peptide index on the protein
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setIndexOnProtein
public void setIndexOnProtein(int indexOnProtein)Sets the peptide index on the protein.- Parameters:
indexOnProtein
- the peptide index on the protein
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getPeptide
Returns a peptide from the peptide draft.- Parameters:
massMin
- the minimal massmassMax
- the maximal mass- Returns:
- the peptide built from the peptide draft
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getPeptide
Returns a peptide from the peptide draft.- Parameters:
massMin
- the minimal massmassMax
- the maximal masssmallMass
- an encapsulated boolean indicating whether the peptide passed the maximal mass filter- Returns:
- the peptide built from the peptide draft
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getFixedModifications
Returns the fixed modifications for the peptide.- Returns:
- the fixed modifications for the peptide.
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