public class Protein extends ExperimentObject
Constructor and Description |
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Protein()
Constructor for a protein.
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Protein(java.lang.String accession,
boolean isDecoy)
Simplistic constructor for a protein (typically used when loading
identification files).
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Protein(java.lang.String accession,
Header.DatabaseType databaseType,
java.lang.String sequence,
boolean isDecoy)
Constructor for a protein.
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Protein(java.lang.String accession,
java.lang.String sequence,
boolean isDecoy)
Constructor for a protein.
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Modifier and Type | Method and Description |
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double |
computeMolecularWeight()
Returns the protein's molecular weight.
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java.lang.String |
getAccession()
Getter for the protein accession.
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Header.DatabaseType |
getDatabaseType()
Getter for the protein database type.
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int |
getLength()
Returns the number of amino acids in the sequence.
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int |
getNCleavageSites(Enzyme enzyme)
Returns the number of cleavage sites.
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int |
getObservableLength(Enzyme enzyme,
int pepMaxLength)
Returns the number of observable amino acids in the sequence.
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java.util.ArrayList<java.lang.Integer> |
getPeptideStart(java.lang.String peptideSequence,
ProteinMatch.MatchingType matchingType,
java.lang.Double massTolerance)
Returns the list of indexes where a peptide can be found in the protein
sequence.
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java.lang.String |
getProteinKey()
Returns the key for protein indexing.
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java.lang.String |
getSequence()
Getter for the protein sequence.
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java.util.HashMap<java.lang.Integer,java.lang.String[]> |
getSurroundingAA(java.lang.String peptide,
int nAA,
ProteinMatch.MatchingType matchingType,
java.lang.Double massTolerance)
Returns the amino acids surrounding a peptide in the sequence of the
given protein in a map: peptide start index -> (amino acids before, amino
acids after).
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boolean |
isCTerm(java.lang.String peptideSequence,
ProteinMatch.MatchingType matchingType,
java.lang.Double massTolerance)
Returns a boolean indicating whether the protein ends with the given
peptide.
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boolean |
isDecoy()
Indicates if the protein is factice (from a decoy database for instance).
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boolean |
isEnzymaticPeptide(java.lang.String peptideSequence,
Enzyme enzyme,
ProteinMatch.MatchingType matchingType,
java.lang.Double massTolerance)
Returns true of the peptide is non-enzymatic, i.e., has one or more end
points that cannot be caused by the enzyme alone.
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boolean |
isNTerm(java.lang.String peptideSequence,
ProteinMatch.MatchingType matchingType,
java.lang.Double massTolerance)
Returns a boolean indicating whether the protein starts with the given
peptide.
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boolean |
isSameAs(Protein anotherProtein)
A method to compare proteins.
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addUrParam, getParameterKey, getUrParam
public Protein()
public Protein(java.lang.String accession, boolean isDecoy)
accession
- The protein accessionisDecoy
- boolean indicating whether the protein is a decoypublic Protein(java.lang.String accession, java.lang.String sequence, boolean isDecoy)
accession
- The protein accessionsequence
- The protein sequenceisDecoy
- boolean indicating whether the protein is a decoypublic Protein(java.lang.String accession, Header.DatabaseType databaseType, java.lang.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 decoypublic boolean isDecoy()
public java.lang.String getAccession()
public Header.DatabaseType getDatabaseType()
public java.lang.String getSequence()
public boolean isSameAs(Protein anotherProtein)
anotherProtein
- an other proteinpublic java.lang.String getProteinKey()
public int getLength()
public int getObservableLength(Enzyme enzyme, int pepMaxLength)
enzyme
- the enzyme to usepepMaxLength
- the max peptide lengthpublic int getNCleavageSites(Enzyme enzyme)
enzyme
- The selected enzymepublic double computeMolecularWeight()
public java.util.ArrayList<java.lang.Integer> getPeptideStart(java.lang.String peptideSequence, ProteinMatch.MatchingType matchingType, java.lang.Double massTolerance)
peptideSequence
- the sequence of the peptide of interestmatchingType
- the type of sequence matchingmassTolerance
- the mass tolerance for matching type
'indistiguishibleAminoAcids'. Can be null otherwisepublic boolean isNTerm(java.lang.String peptideSequence, ProteinMatch.MatchingType matchingType, java.lang.Double massTolerance)
peptideSequence
- the peptide sequencematchingType
- the type of sequence matchingmassTolerance
- the mass tolerance for matching type
'indistiguishibleAminoAcids'. Can be null otherwisepublic boolean isCTerm(java.lang.String peptideSequence, ProteinMatch.MatchingType matchingType, java.lang.Double massTolerance)
peptideSequence
- the peptide sequencematchingType
- the type of sequence matchingmassTolerance
- the mass tolerance for matching type
'indistiguishibleAminoAcids'. Can be null otherwisepublic boolean isEnzymaticPeptide(java.lang.String peptideSequence, Enzyme enzyme, ProteinMatch.MatchingType matchingType, java.lang.Double massTolerance) throws java.io.IOException
peptideSequence
- the peptide sequence to checkenzyme
- the enzyme to usematchingType
- the type of sequence matchingmassTolerance
- the mass tolerance for matching type
'indistiguishibleAminoAcids'. Can be null otherwisejava.io.IOException
public java.util.HashMap<java.lang.Integer,java.lang.String[]> getSurroundingAA(java.lang.String peptide, int nAA, ProteinMatch.MatchingType matchingType, java.lang.Double massTolerance) throws java.io.IOException
peptide
- the sequence of the peptide of interestnAA
- the number of amino acids to includematchingType
- the type of sequence matchingmassTolerance
- the mass tolerance for matching type
'indistiguishibleAminoAcids'. Can be null otherwisejava.io.IOException
- Exception thrown whenever an error occurred while
parsing the protein sequenceCopyright © 2013. All Rights Reserved.