|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.Protein
public class Protein
This class models a protein.
Constructor Summary | |
---|---|
Protein()
Constructor for a protein. |
|
Protein(String accession,
boolean isDecoy)
Simplistic constructor for a protein (typically used when loading identification files). |
|
Protein(String accession,
Header.DatabaseType databaseType,
String sequence,
boolean isDecoy)
Constructor for a protein. |
|
Protein(String accession,
String sequence,
boolean isDecoy)
Constructor for a protein. |
Method Summary | |
---|---|
double |
computeMolecularWeight()
Returns the protein's molecular weight. |
String |
getAccession()
Getter for the protein accession. |
Header.DatabaseType |
getDatabaseType()
Getter for the protein database type. |
int |
getLength()
Returns the number of amino acids in the sequence. |
int |
getNCleavageSites(Enzyme enzyme)
Returns the number of cleavage sites. |
int |
getObservableLength(Enzyme enzyme,
int pepMaxLength)
Returns the number of observable amino acids in the sequence. |
ArrayList<Integer> |
getPeptideStart(String peptideSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns the list of indexes where a peptide can be found in the protein sequence. |
String |
getProteinKey()
Returns the key for protein indexing. |
String |
getSequence()
Getter for the protein sequence. |
HashMap<Integer,String[]> |
getSurroundingAA(String peptide,
int nAA,
ProteinMatch.MatchingType matchingType,
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). |
boolean |
isCTerm(String peptideSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns a boolean indicating whether the protein ends with the given peptide. |
boolean |
isDecoy()
Indicates if the protein is factice (from a decoy database for instance). |
boolean |
isEnzymaticPeptide(String peptideSequence,
Enzyme enzyme,
ProteinMatch.MatchingType matchingType,
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. |
boolean |
isNTerm(String peptideSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns a boolean indicating whether the protein starts with the given peptide. |
boolean |
isSameAs(Protein anotherProtein)
A method to compare proteins. |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
---|
addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
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, Header.DatabaseType 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 |
---|
public boolean isDecoy()
public String getAccession()
public Header.DatabaseType getDatabaseType()
public String getSequence()
public boolean isSameAs(Protein anotherProtein)
anotherProtein
- an other protein
public String getProteinKey()
public int getLength()
public int getObservableLength(Enzyme enzyme, int pepMaxLength)
enzyme
- the enzyme to usepepMaxLength
- the max peptide length
public int getNCleavageSites(Enzyme enzyme)
enzyme
- The selected enzyme
public double computeMolecularWeight()
public ArrayList<Integer> getPeptideStart(String peptideSequence, ProteinMatch.MatchingType matchingType, 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 otherwise
public boolean isNTerm(String peptideSequence, ProteinMatch.MatchingType matchingType, Double massTolerance)
peptideSequence
- the peptide sequencematchingType
- the type of sequence matchingmassTolerance
- the mass tolerance for matching type
'indistiguishibleAminoAcids'. Can be null otherwise
public boolean isCTerm(String peptideSequence, ProteinMatch.MatchingType matchingType, Double massTolerance)
peptideSequence
- the peptide sequencematchingType
- the type of sequence matchingmassTolerance
- the mass tolerance for matching type
'indistiguishibleAminoAcids'. Can be null otherwise
public boolean isEnzymaticPeptide(String peptideSequence, Enzyme enzyme, ProteinMatch.MatchingType matchingType, Double massTolerance) throws 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 otherwise
IOException
public HashMap<Integer,String[]> getSurroundingAA(String peptide, int nAA, ProteinMatch.MatchingType matchingType, Double massTolerance) throws 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 otherwise
IOException
- Exception thrown whenever an error occurred while
parsing the protein sequence
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |