public class PeptideEvidence extends IdentifiableParamGroup
The Peptide Evidence Element contains the following information: - start position: Start position of the peptide inside the protein sequence. - end position: The index position of the last amino acid of the peptide inside the protein sequence. - preResidue and posResidue: Previous and Post flanking residues. - decoy: Set to true if the peptide is matched to a decoy sequence. - peptide Reference: The reference to the Peptide Sequence in the Database. - Protein Reference: The reference to the Protein or Nucleotide Sequence in the database. - frame: The translation frame of this sequence if this is PeptideEvidence derived from nucleic acid sequence. - Translation Table: A reference to the translation table used if this is PeptideEvidence derived from nucleic acid sequence
Constructor and Description |
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PeptideEvidence(ParamGroup params,
String id,
String name,
Integer startPosition,
Integer endPosition,
boolean decoy,
PeptideSequence peptideSequence,
DBSequence dbSequence) |
PeptideEvidence(String id,
String name,
Integer startPosition,
Integer endPosition,
Boolean decoy,
PeptideSequence peptideSequence,
DBSequence dbSequence) |
Modifier and Type | Method and Description |
---|---|
boolean |
equals(Object o) |
DBSequence |
getDbSequence() |
Integer |
getEndPosition() |
int |
getFrame() |
PeptideSequence |
getPeptideSequence() |
char |
getPostResidue() |
char |
getPreResidue() |
Integer |
getStartPosition() |
IdentifiableParamGroup |
getTranslationTable() |
int |
hashCode() |
boolean |
isDecoy() |
void |
setDbSequence(DBSequence dbSequence) |
void |
setDecoy(boolean decoy) |
void |
setEndPosition(int endPosition) |
void |
setFrame(int frame) |
void |
setPeptideSequence(PeptideSequence peptideSequence) |
void |
setPostResidue(char postResidue) |
void |
setPreResidue(char preResidue) |
void |
setStartPosition(int startPosition) |
void |
setTranslationTable(IdentifiableParamGroup translationTable) |
getId, getName, setId, setName, toString
addCvParam, addCvParams, addUserParam, addUserParams, getCvParams, getUserParams, isEmpty, removeCvParam, removeCvParams, removeUserParam, removeUserParams, setCvParams, setUserParams
public PeptideEvidence(String id, String name, Integer startPosition, Integer endPosition, Boolean decoy, PeptideSequence peptideSequence, DBSequence dbSequence)
public PeptideEvidence(ParamGroup params, String id, String name, Integer startPosition, Integer endPosition, boolean decoy, PeptideSequence peptideSequence, DBSequence dbSequence)
public Integer getStartPosition()
public void setStartPosition(int startPosition)
public Integer getEndPosition()
public void setEndPosition(int endPosition)
public char getPreResidue()
public void setPreResidue(char preResidue)
public char getPostResidue()
public void setPostResidue(char postResidue)
public int getFrame()
public void setFrame(int frame)
public boolean isDecoy()
public void setDecoy(boolean decoy)
public PeptideSequence getPeptideSequence()
public void setPeptideSequence(PeptideSequence peptideSequence)
public DBSequence getDbSequence()
public void setDbSequence(DBSequence dbSequence)
public IdentifiableParamGroup getTranslationTable()
public void setTranslationTable(IdentifiableParamGroup translationTable)
public boolean equals(Object o)
equals
in class IdentifiableParamGroup
public int hashCode()
hashCode
in class IdentifiableParamGroup
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.