public class Protein extends IdentifiableParamGroup
Constructor and Description |
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Protein(Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel)
Constructor for Protein Entity Identification
|
Protein(ParamGroup params,
Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel)
Constructor for Protein Entity Identification with CVParams
|
Protein(ParamGroup params,
Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel,
QuantScore quantScore)
Constructor for Protein Entity Identification with CVParams and Quantitation Score based on mzTab model
|
Protein(ParamGroup params,
Comparable id,
String name,
DBSequence dbSequence,
boolean passThreshold,
List<Peptide> peptides,
Score score,
double threshold,
double sequenceCoverage,
Gel gel,
QuantScore quantScore,
List<QuantPeptide> quantPeptides)
Constructor for Protein Entity Identification with CVParams and Quantitation Score based on mzTab model
|
Modifier and Type | Method and Description |
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boolean |
equals(Object o) |
DBSequence |
getDbSequence() |
Gel |
getGel() |
List<Peptide> |
getPeptides() |
List<PeptideSequence> |
getPeptidesSequence() |
List<QuantPeptide> |
getQuantPeptides() |
QuantScore |
getQuantScore() |
Score |
getScore() |
double |
getSequenceCoverage() |
double |
getThreshold() |
int |
hashCode() |
boolean |
isPassThreshold() |
void |
setDbSequence(DBSequence dbSequence) |
void |
setGel(Gel gel) |
void |
setPassThreshold(boolean passThreshold) |
void |
setPeptides(List<Peptide> peptides) |
void |
setQuantScore(QuantScore quantScore) |
void |
setScore(Score score) |
void |
setSequenceCoverage(double sequenceCoverage) |
void |
setThreshold(double threshold) |
getId, getName, setId, setName, toString
addCvParam, addCvParams, addUserParam, addUserParams, getCvParams, getUserParams, isEmpty, removeCvParam, removeCvParams, removeUserParam, removeUserParams, setCvParams, setUserParams
public Protein(Comparable id, String name, DBSequence dbSequence, boolean passThreshold, List<Peptide> peptides, Score score, double threshold, double sequenceCoverage, Gel gel)
id
- Protein Idname
- Name of the proteindbSequence
- DBSequence referencing the Database entitypassThreshold
- If pass the Threshold or notpeptides
- List of peptides that reference the proteinscore
- Identification Proteinthreshold
- Threshold apply to the protein that passsequenceCoverage
- Sequence coveragegel
- Reference to the Gel entitypublic Protein(ParamGroup params, Comparable id, String name, DBSequence dbSequence, boolean passThreshold, List<Peptide> peptides, Score score, double threshold, double sequenceCoverage, Gel gel)
id
- Protein Idname
- Name of the proteindbSequence
- DBSequence referencing the Database entitypassThreshold
- If pass the Threshold or notpeptides
- List of peptides that reference the proteinscore
- Identification Proteinthreshold
- Threshold apply to the protein that passsequenceCoverage
- Sequence coveragegel
- Reference to the Gel entitypublic Protein(ParamGroup params, Comparable id, String name, DBSequence dbSequence, boolean passThreshold, List<Peptide> peptides, Score score, double threshold, double sequenceCoverage, Gel gel, QuantScore quantScore)
id
- Protein Idname
- Name of the proteindbSequence
- DBSequence referencing the Database entitypassThreshold
- If pass the Threshold or notpeptides
- List of peptides that reference the proteinscore
- Identification Proteinthreshold
- Threshold apply to the protein that passsequenceCoverage
- Sequence coveragegel
- Reference to the Gel entityquantScore
- The quantitative Scores (Study Variables and Abundance Scores)public Protein(ParamGroup params, Comparable id, String name, DBSequence dbSequence, boolean passThreshold, List<Peptide> peptides, Score score, double threshold, double sequenceCoverage, Gel gel, QuantScore quantScore, List<QuantPeptide> quantPeptides)
id
- Protein Idname
- Name of the proteindbSequence
- DBSequence referencing the Database entitypassThreshold
- If pass the Threshold or notpeptides
- List of peptides that reference the proteinscore
- Identification Proteinthreshold
- Threshold apply to the protein that passsequenceCoverage
- Sequence coveragegel
- Reference to the Gel entityquantScore
- Quantitation Score for proteinsquantPeptides
- List of Quantitative Peptidespublic DBSequence getDbSequence()
public void setDbSequence(DBSequence dbSequence)
public boolean isPassThreshold()
public void setPassThreshold(boolean passThreshold)
public Score getScore()
public void setScore(Score score)
public double getThreshold()
public void setThreshold(double threshold)
public double getSequenceCoverage()
public void setSequenceCoverage(double sequenceCoverage)
public List<PeptideSequence> getPeptidesSequence()
public Gel getGel()
public void setGel(Gel gel)
public QuantScore getQuantScore()
public void setQuantScore(QuantScore quantScore)
public List<QuantPeptide> getQuantPeptides()
public boolean equals(Object o)
equals
in class IdentifiableParamGroup
public int hashCode()
hashCode
in class IdentifiableParamGroup
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.