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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.Protein
public class Protein
This class models a protein. Created by IntelliJ IDEA. User: Marc Date: Jun 18, 2010 Time: 8:56:22 AM
Constructor Summary | |
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Protein()
Constructor for a protein |
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Protein(String accession,
boolean isDecoy)
Simplistic constructor for a protein (typically used when loading identification files). |
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Protein(String accession,
String sequence,
boolean isDecoy)
Constructor for a protein. |
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Protein(String accession,
String databaseType,
String sequence,
boolean isDecoy)
Constructor for a protein. |
Method Summary | |
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String |
getAccession()
Getter for the protein accession |
String |
getDatabaseType()
Getter for the protein database type. |
int |
getNPossiblePeptides(Enzyme enzyme)
Returns the number of possible peptides (not accounting PTMs nor missed cleavages) with the selected enzyme |
String |
getProteinKey()
Returns the key for protein indexing. |
String |
getSequence()
Getter for the protein sequence |
boolean |
isDecoy()
Indicates if the protein is factice (from a decoy database for instance) |
boolean |
isSameAs(Protein anotherProtein)
A method to compare proteins. |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Protein()
public Protein(String accession, boolean isDecoy)
accession
- The protein accessionisDecoy
- boolean indicating whether the protein is a decoypublic Protein(String accession, String sequence, boolean isDecoy)
accession
- The protein accessionsequence
- The protein sequenceisDecoy
- boolean indicating whether the protein is a decoypublic Protein(String accession, String databaseType, String sequence, boolean isDecoy)
accession
- The protein accessiondatabaseType
- The protein database the protein comes fromsequence
- The protein sequenceisDecoy
- boolean indicating whether the protein is a decoyMethod Detail |
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public boolean isDecoy()
public String getAccession()
public String getDatabaseType()
public String getSequence()
public boolean isSameAs(Protein anotherProtein)
anotherProtein
- an other protein
public String getProteinKey()
public int getNPossiblePeptides(Enzyme enzyme)
enzyme
- The selected enzyme
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