public class PeptideDraft extends Object
Constructor and Description |
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PeptideDraft(char[] sequence)
Constructor.
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PeptideDraft(char[] sequence,
String nTermModification,
HashMap<Integer,String> fixedAaModifications,
double mass)
Constructor.
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PeptideDraft(char[] sequence,
String nTermModification,
HashMap<Integer,String> fixedAaModifications,
double mass,
int missedCleavages)
Constructor.
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PeptideDraft(char[] sequence,
String nTermModification,
String cTermModification,
HashMap<Integer,String> fixedAaModifications,
double mass)
Constructor.
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PeptideDraft(char[] sequence,
String nTermModification,
String cTermModification,
HashMap<Integer,String> fixedAaModifications,
double mass,
int missedCleavages)
Constructor.
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Modifier and Type | Method and Description |
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PeptideDraft |
clone()
Creates a new peptide draft with the same attributes as this one.
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String |
getcTermModification()
Returns the C-term modification.
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HashMap<Integer,String> |
getFixedAaModifications()
Returns the modifications at specific amino acids.
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int |
getIndexOnProtein()
Returns the peptide index on the protein.
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double |
getMass()
Returns the mass.
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int |
getMissedCleavages()
Returns the number of missed cleavages.
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String |
getnTermModification()
Returns the N-term modification.
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int |
getnX()
Returns the number of Xs already considered in this draft.
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Peptide |
getPeptide(double massMin,
double massMax)
Returns a peptide from the peptide draft.
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Peptide |
getPeptide(double massMin,
double massMax,
BoxedObject<Boolean> smallMass)
Returns a peptide from the peptide draft.
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char[] |
getSequence()
Returns the sequence.
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void |
increaseMissedCleavages()
Increases the number of missed cleavages.
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void |
increaseNX()
Increases the number of Xs already considered in this draft.
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int |
length()
Returns the length of the sequence.
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void |
setcTermModification(String cTermModification)
Sets the C-term modification.
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void |
setFixedAaModifications(HashMap<Integer,String> fixedAaModifications)
Sets the modifications at specific amino acids.
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void |
setIndexOnProtein(int indexOnProtein)
Sets the peptide index on the protein.
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void |
setMass(double mass)
Sets the mass.
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void |
setnTermModification(String nTermModification)
Sets the N-term modification.
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void |
setSequence(char[] sequence)
Sets the sequence.
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public PeptideDraft(char[] sequence)
sequence
- the peptide sequence.public PeptideDraft(char[] sequence, String nTermModification, HashMap<Integer,String> fixedAaModifications, double mass)
sequence
- the peptide sequencenTermModification
- the N-term modificationfixedAaModifications
- the fixed modifications at amino acidsmass
- the masspublic PeptideDraft(char[] sequence, String nTermModification, HashMap<Integer,String> fixedAaModifications, double mass, int missedCleavages)
sequence
- the peptide sequencenTermModification
- the N-term modificationfixedAaModifications
- the fixed modifications at amino acidsmass
- the massmissedCleavages
- the number of missed cleavagespublic PeptideDraft(char[] sequence, String nTermModification, String cTermModification, HashMap<Integer,String> fixedAaModifications, double mass)
sequence
- the peptide sequencenTermModification
- the N-term modificationcTermModification
- the C-term modificationfixedAaModifications
- the fixed modifications at amino acidsmass
- the masspublic PeptideDraft(char[] sequence, String nTermModification, String cTermModification, HashMap<Integer,String> fixedAaModifications, double mass, int missedCleavages)
sequence
- the peptide sequencenTermModification
- the N-term modificationcTermModification
- the C-term modificationfixedAaModifications
- the fixed modifications at amino acidsmass
- the massmissedCleavages
- the number of missed cleavagespublic PeptideDraft clone()
public char[] getSequence()
public void setSequence(char[] sequence)
sequence
- the sequencepublic int length()
public String getnTermModification()
public void setnTermModification(String nTermModification)
nTermModification
- the N-term modificationpublic String getcTermModification()
public void setcTermModification(String cTermModification)
cTermModification
- the C-term modificationpublic double getMass()
public void setMass(double mass)
mass
- the masspublic HashMap<Integer,String> getFixedAaModifications()
public void setFixedAaModifications(HashMap<Integer,String> fixedAaModifications)
fixedAaModifications
- the modifications at specific amino acidspublic void increaseMissedCleavages()
public int getMissedCleavages()
public void increaseNX()
public int getnX()
public int getIndexOnProtein()
public void setIndexOnProtein(int indexOnProtein)
indexOnProtein
- the peptide index on the proteinpublic Peptide getPeptide(double massMin, double massMax)
massMin
- the minimal massmassMax
- the maximal masspublic Peptide getPeptide(double massMin, double massMax, BoxedObject<Boolean> smallMass)
massMin
- the minimal massmassMax
- the maximal masssmallMass
- an encapsulated boolean indicating whether the peptide
passed the maximal mass filterCopyright © 2019. All rights reserved.