com.compomics.util.experiment.biology

Class Peptide

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.biology.Peptide

All Implemented Interfaces:

Serializable, Cloneable

public class Peptide
extends ExperimentObject

This class models a peptide.

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	MODIFICATION_LOCALIZATION_SEPARATOR Separator preceding confident localization of the confident localization of a modification
static String	MODIFICATION_SEPARATOR Separator used to separate modifications in peptide keys

Constructor Summary

Constructors

Constructor and Description
Peptide() Constructor for the peptide.
Peptide(String aSequence, ArrayList<ModificationMatch> modifications) Constructor for the peptide.
Peptide(String aSequence, ArrayList<String> parentProteins, ArrayList<ModificationMatch> modifications) Deprecated. use peptide without proteins and remap the peptide to the proteins a posteriori instead
Peptide(String aSequence, Double mass, ArrayList<String> parentProteins, ArrayList<ModificationMatch> modifications) Deprecated. use the constructor without mass. The mass will be recalculated.

Method Summary

Methods

Modifier and Type	Method and Description
void	addModificationMatch(ModificationMatch modificationMatch) Adds a modification match.
void	clearModificationMatches() Clears the list of imported modification matches.
void	estimateTheoreticMass() Estimates the theoretic mass of the peptide.
String	getCTerminal() Returns the C-terminal of the peptide as a String.
HashMap<Integer,ArrayList<String>>	getIndexedFixedModifications() Returns an indexed map of all fixed modifications amino acid, (1 is the first) -> list of modification names.
String	getKey() Returns the reference key of a peptide.
static String	getKey(String sequence, ArrayList<ModificationMatch> modificationMatches) Returns the reference key of a peptide.
Double	getMass() Getter for the mass.
String	getMatchingKey(AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns a unique key for the peptide when considering the given matching type and mass tolerance.
static int	getModificationCount(String peptideKey, String modification) Returns how many of the given modification was found in the given peptide.
static ArrayList<String>	getModificationFamily(String peptideKey) Returns a list of names of the variable modifications found in the key of a peptide.
ArrayList<ModificationMatch>	getModificationMatches() Getter for the modifications carried by this peptide.
ArrayList<Integer>	getModifiedIndexes() Returns the indexes of the residues in the peptide that contain at least one variable modification.
ArrayList<Integer>	getModifiedIndexes(boolean excludeFixed) Returns the indexes of the residues in the peptide that contain at least one modification.
int	getNMissedCleavages(Enzyme enzyme) Returns the number of missed cleavages using the specified enzyme.
static int	getNMissedCleavages(String sequence, Enzyme enzyme) Returns the number of missed cleavages using the specified enzyme for the given sequence.
static ArrayList<Integer>	getNModificationLocalized(String peptideKey, String modification) Returns the list of modifications confidently localized or inferred for the peptide indexed by the given key.
static Peptide	getNoModPeptide(Peptide peptide, ArrayList<PTM> ptms) Returns a version of the peptide which does not contain the inspected PTMs.
String	getNTerminal() Returns the N-terminal of the peptide as a String.
int	getNVariableModifications(double modificationMass) Returns the number of variable modifications found with the given mass.
ArrayList<String>	getParentProteins(AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns the parent proteins and remaps the peptide to the protein if no protein mapping was set using the default protein tree of the sequence factory.
ArrayList<String>	getParentProteins(AminoAcidPattern.MatchingType matchingType, Double massTolerance, ProteinTree proteinTree) Returns the parent proteins and remaps the peptide to the protein if no protein mapping was set.
ArrayList<String>	getParentProteins(boolean remap, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns the parent proteins and eventually remaps the peptide to the protein using the default protein tree.
ArrayList<String>	getParentProteins(boolean remap, AminoAcidPattern.MatchingType matchingType, Double massTolerance, ProteinTree proteinTree) Returns the parent proteins and eventually remaps the peptide to the protein.
ArrayList<String>	getParentProteinsNoRemapping() Returns the parent proteins without remapping them.
ArrayList<Integer>	getPotentialModificationSites(Double ptmMass, AminoAcidPattern.MatchingType matchingType, Double massTolerance, ModificationProfile modificationProfile) Returns the potential modification sites as an ordered list of string.
ArrayList<Integer>	getPotentialModificationSites(PTM ptm, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns the potential modification sites as an ordered list of string.
static ArrayList<Integer>	getPotentialModificationSites(String sequence, PTM ptm) Deprecated. use getPotentialModificationSites(PTM ptm, AminoAcidPattern.MatchingType matchingType, Double massTolerance)
String	getSequence() Getter for the sequence.
static String	getSequence(String peptideKey) Returns the sequence of the peptide indexed by the given key.
AminoAcidPattern	getSequenceAsPattern() Returns the sequence of this peptide as AminoAcidPattern.
static AminoAcidPattern	getSequenceAsPattern(String sequence) Returns the given sequence as AminoAcidPattern.
String	getTaggedModifiedSequence(ModificationProfile modificationProfile, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName) Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
String	getTaggedModifiedSequence(ModificationProfile modificationProfile, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName, boolean excludeAllFixedPtms) Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
static String	getTaggedModifiedSequence(ModificationProfile modificationProfile, Peptide peptide, HashMap<Integer,ArrayList<String>> mainModificationSites, HashMap<Integer,ArrayList<String>> secondaryModificationSites, HashMap<Integer,ArrayList<String>> fixedModificationSites, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName) Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>.
ArrayList<String>	isCterm(AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns a list of proteins where this peptide can be found in the C-terminus.
boolean	isDecoy(AminoAcidPattern.MatchingType matchingType, Double massTolerance) Indicates whether a peptide can be derived from a decoy protein.
boolean	isModifiable(PTM ptm, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Indicates whether the given modification can be found on the peptide.
static boolean	isModified(String peptideKey) Returns a boolean indicating whether the peptide has variable modifications based on its key.
static boolean	isModified(String peptideKey, String modification) Returns a boolean indicating whether the peptide has the given variable modification based on its key.
ArrayList<String>	isNterm(AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns a list of proteins where this peptide can be found in the N-terminus.
boolean	isSameModificationStatus(Peptide anotherPeptide) Indicates whether another peptide has the same variable modifications as this peptide.
boolean	isSameSequence(Peptide anotherPeptide, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns a boolean indicating whether another peptide has the same sequence as the given peptide
boolean	isSameSequenceAndModificationStatus(Peptide anotherPeptide, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Indicates whether another peptide has the same sequence and modification status without accounting for modification localization.
boolean	sameModificationsAs(Peptide anotherPeptide) Indicates whether another peptide has the same modifications at the same localization as this peptide.
boolean	sameModificationsAs(Peptide anotherPeptide, ArrayList<String> ptms) Indicates whether another peptide has the same modifications at the same localization as this peptide.
void	setParentProteins(ArrayList<String> parentProteins) Sets the parent 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

Field Detail

MODIFICATION_LOCALIZATION_SEPARATOR

public static final String MODIFICATION_LOCALIZATION_SEPARATOR

Separator preceding confident localization of the confident localization of a modification

See Also:

Constant Field Values

MODIFICATION_SEPARATOR

public static final String MODIFICATION_SEPARATOR

Separator used to separate modifications in peptide keys

See Also:

Constant Field Values

Constructor Detail

Peptide

public Peptide()

Constructor for the peptide.

Peptide

public Peptide(String aSequence,
       ArrayList<String> parentProteins,
       ArrayList<ModificationMatch> modifications)
        throws IllegalArgumentException

Deprecated. use peptide without proteins and remap the peptide to the proteins a posteriori instead

Constructor for the peptide.

Parameters:

aSequence - The peptide sequence

parentProteins - The parent proteins, cannot be null or empty

modifications - The PTM of this peptide

Throws:

IllegalArgumentException - Thrown if the peptide sequence contains unknown amino acids

Peptide

public Peptide(String aSequence,
       ArrayList<ModificationMatch> modifications)
        throws IllegalArgumentException

Constructor for the peptide.

Parameters:

aSequence - The peptide sequence

modifications - The PTM of this peptide

Throws:

IllegalArgumentException - Thrown if the peptide sequence contains unknown amino acids

Peptide

public Peptide(String aSequence,
       Double mass,
       ArrayList<String> parentProteins,
       ArrayList<ModificationMatch> modifications)

Deprecated. use the constructor without mass. The mass will be recalculated.

Constructor for the peptide.

Parameters:

aSequence - The peptide sequence

mass - The peptide mass

parentProteins - The parent proteins, cannot be null or empty

modifications - The PTM of this peptide

Method Detail

getMass

public Double getMass()

Getter for the mass.

Returns:

the peptide mass

getModificationMatches

public ArrayList<ModificationMatch> getModificationMatches()

Getter for the modifications carried by this peptide.

Returns:

the modifications matches as found by the search engine

clearModificationMatches

public void clearModificationMatches()

Clears the list of imported modification matches.

addModificationMatch

public void addModificationMatch(ModificationMatch modificationMatch)

Adds a modification match.

Parameters:

modificationMatch - the modification match to add

getSequence

public String getSequence()

Getter for the sequence.

Returns:

the peptide sequence

getNMissedCleavages

public int getNMissedCleavages(Enzyme enzyme)

Returns the number of missed cleavages using the specified enzyme.

Parameters:

enzyme - the enzyme used

Returns:

the amount of missed cleavages

getNMissedCleavages

public static int getNMissedCleavages(String sequence,
                      Enzyme enzyme)

Returns the number of missed cleavages using the specified enzyme for the given sequence.

Parameters:

sequence - the peptide sequence

enzyme - the enzyme used

Returns:

the amount of missed cleavages

getParentProteins

public ArrayList<String> getParentProteins(boolean remap,
                                  AminoAcidPattern.MatchingType matchingType,
                                  Double massTolerance)
                                    throws IOException,
                                           ClassNotFoundException,
                                           InterruptedException,
                                           SQLException

Returns the parent proteins and eventually remaps the peptide to the protein using the default protein tree.

Parameters:

remap - boolean indicating whether the peptide sequence should be remapped to the proteins if no protein is found

matchingType - the desired peptide to protein matching type

massTolerance - the ms2 mass tolerance

Returns:

the proteins mapping this peptide

Throws:

IOException

ClassNotFoundException

InterruptedException

SQLException

getParentProteins

public ArrayList<String> getParentProteins(AminoAcidPattern.MatchingType matchingType,
                                  Double massTolerance,
                                  ProteinTree proteinTree)
                                    throws IOException,
                                           InterruptedException,
                                           SQLException,
                                           ClassNotFoundException

Returns the parent proteins and remaps the peptide to the protein if no protein mapping was set.

Parameters:

matchingType - the desired peptide to protein matching type

massTolerance - the ms2 mass tolerance

proteinTree - the protein tree to use for peptide to protein mapping

Returns:

the proteins mapping this peptide

Throws:

IOException

ClassNotFoundException

InterruptedException

SQLException

getParentProteins

public ArrayList<String> getParentProteins(AminoAcidPattern.MatchingType matchingType,
                                  Double massTolerance)
                                    throws IOException,
                                           InterruptedException,
                                           SQLException,
                                           ClassNotFoundException

Returns the parent proteins and remaps the peptide to the protein if no protein mapping was set using the default protein tree of the sequence factory.

Parameters:

matchingType - the desired peptide to protein matching type

massTolerance - the ms2 mass tolerance

Returns:

the proteins mapping this peptide

Throws:

IOException

ClassNotFoundException

InterruptedException

SQLException

getParentProteins

public ArrayList<String> getParentProteins(boolean remap,
                                  AminoAcidPattern.MatchingType matchingType,
                                  Double massTolerance,
                                  ProteinTree proteinTree)
                                    throws IOException,
                                           InterruptedException,
                                           SQLException,
                                           ClassNotFoundException

Returns the parent proteins and eventually remaps the peptide to the protein. Note, the maximal share of 'X's in the sequence is set according to the ProteinMatch MaxX field.

Parameters:

remap - boolean indicating whether the peptide sequence should be remapped to the proteins if no protein is found

matchingType - the desired peptide to protein matching type

massTolerance - the ms2 mass tolerance

proteinTree - the protein tree to use for peptide to protein mapping

Returns:

the proteins mapping this peptide

Throws:

IOException

ClassNotFoundException

InterruptedException

SQLException

getParentProteinsNoRemapping

public ArrayList<String> getParentProteinsNoRemapping()

Returns the parent proteins without remapping them. Null if none mapped.

Returns:

an ArrayList containing the parent proteins

setParentProteins

public void setParentProteins(ArrayList<String> parentProteins)

Sets the parent proteins.

Parameters:

parentProteins - the parent proteins as list, cannot be null or empty

getMatchingKey

public String getMatchingKey(AminoAcidPattern.MatchingType matchingType,
                    Double massTolerance)

Returns a unique key for the peptide when considering the given matching type and mass tolerance. when ambiguity the first amino acid according to AminoAcid.getAminoAcidsList() will be selected. For example the matching key of peptide PEPTLDE_mod1_mod2 is PEPTIDE_mod1_mod2

Parameters:

matchingType - the amino acid matching type

massTolerance - the mass tolerance

Returns:

a key unique to the given matching type

getKey

public String getKey()

Returns the reference key of a peptide. index = SEQUENCE_mod1_mod2 with modifications ordered alphabetically. Note: the key is not unique for indistinguishable sequences, see getMatchingKey(AminoAcidPattern.MatchingType matchingType, Double massTolerance).

Returns:

the index of a peptide

getKey

public static String getKey(String sequence,
            ArrayList<ModificationMatch> modificationMatches)

Returns the reference key of a peptide. key = SEQUENCE_mod1_mod2 with modifications ordered alphabetically.

Parameters:

sequence - the sequence of the peptide

modificationMatches - list of modification matches

Returns:

the index of a peptide

isModified

public static boolean isModified(String peptideKey)

Returns a boolean indicating whether the peptide has variable modifications based on its key.

Parameters:

peptideKey - the peptide key

Returns:

a boolean indicating whether the peptide has variable modifications

isModified

public static boolean isModified(String peptideKey,
                 String modification)

Returns a boolean indicating whether the peptide has the given variable modification based on its key.

Parameters:

peptideKey - the peptide key

modification - the name of the modification

Returns:

a boolean indicating whether the peptide has variable modifications

getModificationCount

public static int getModificationCount(String peptideKey,
                       String modification)

Returns how many of the given modification was found in the given peptide.

Parameters:

peptideKey - the peptide key

modification - the name of the modification

Returns:

the number of modifications

getNVariableModifications

public int getNVariableModifications(double modificationMass)

Returns the number of variable modifications found with the given mass.

Parameters:

modificationMass - the mass of the modification

Returns:

the number of occurrences of this modification

getNModificationLocalized

public static ArrayList<Integer> getNModificationLocalized(String peptideKey,
                                           String modification)

Returns the list of modifications confidently localized or inferred for the peptide indexed by the given key.

Parameters:

peptideKey - the peptide key

modification - the name of the modification

Returns:

the number of modifications confidently localized

getSequence

public static String getSequence(String peptideKey)

Returns the sequence of the peptide indexed by the given key.

Parameters:

peptideKey - the peptide key

Returns:

the corresponding sequence

getModificationFamily

public static ArrayList<String> getModificationFamily(String peptideKey)

Returns a list of names of the variable modifications found in the key of a peptide.

Parameters:

peptideKey - the key of a peptide

Returns:

a list of names of the variable modifications found in the key

isModifiable

public boolean isModifiable(PTM ptm,
                   AminoAcidPattern.MatchingType matchingType,
                   Double massTolerance)
                     throws IOException,
                            IllegalArgumentException,
                            InterruptedException,
                            FileNotFoundException,
                            ClassNotFoundException,
                            SQLException

Indicates whether the given modification can be found on the peptide. For instance, 'oxidation of M' cannot be found on sequence "PEPTIDE". For the inspection of protein termini and peptide C-terminus the proteins sequences must be accessible from the sequence factory.

Parameters:

ptm - the PTM of interest

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

a boolean indicating whether the given modification can be found on the peptide

Throws:

IOException - exception thrown whenever an error occurred while reading a protein sequence

IllegalArgumentException - exception thrown whenever an error occurred while reading a protein sequence

InterruptedException - exception thrown whenever an error occurred while reading a protein sequence

FileNotFoundException

ClassNotFoundException

SQLException

getPotentialModificationSites

public ArrayList<Integer> getPotentialModificationSites(Double ptmMass,
                                               AminoAcidPattern.MatchingType matchingType,
                                               Double massTolerance,
                                               ModificationProfile modificationProfile)
                                                 throws IOException,
                                                        IllegalArgumentException,
                                                        InterruptedException,
                                                        FileNotFoundException,
                                                        ClassNotFoundException,
                                                        SQLException

Returns the potential modification sites as an ordered list of string. 1 is the first amino acid. An empty list is returned if no possibility was found. This method does not account for protein terminal modifications.

Parameters:

ptmMass - the mass of the potential PTM

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

modificationProfile - the modification profile of the identification

Returns:

a list of potential modification sites

Throws:

IOException - exception thrown whenever an error occurred while reading a protein sequence

IllegalArgumentException - exception thrown whenever an error occurred while reading a protein sequence

InterruptedException - exception thrown whenever an error occurred while reading a protein sequence

FileNotFoundException

ClassNotFoundException

SQLException

getPotentialModificationSites

public ArrayList<Integer> getPotentialModificationSites(PTM ptm,
                                               AminoAcidPattern.MatchingType matchingType,
                                               Double massTolerance)
                                                 throws IOException,
                                                        IllegalArgumentException,
                                                        InterruptedException,
                                                        FileNotFoundException,
                                                        ClassNotFoundException,
                                                        SQLException

Returns the potential modification sites as an ordered list of string. 1 is the first amino acid. An empty list is returned if no possibility was found.

Parameters:

ptm - the PTM considered

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

a list of potential modification sites

Throws:

IOException - exception thrown whenever an error occurred while reading a protein sequence

IllegalArgumentException - exception thrown whenever an error occurred while reading a protein sequence

InterruptedException - exception thrown whenever an error occurred while reading a protein sequence

FileNotFoundException

ClassNotFoundException

SQLException

getPotentialModificationSites

public static ArrayList<Integer> getPotentialModificationSites(String sequence,
                                               PTM ptm)
                                                        throws IllegalArgumentException

Deprecated. use getPotentialModificationSites(PTM ptm, AminoAcidPattern.MatchingType matchingType, Double massTolerance)

Returns the potential modification sites as an ordered list of string. 1 is the first aa. an empty list is returned if no possibility was found. This method does not account for protein terminal modifications. Only works if the modification pattern can be fully found in the sequence (single amino acid or terminal patterns smaller than the sequence). Otherwise an IllegalArgumentException will be thrown. Use the non static method then.

Parameters:

sequence - the sequence of the peptide of interest

ptm - the PTM considered

Returns:

a list of potential modification sites

Throws:

IllegalArgumentException

isSameSequenceAndModificationStatus

public boolean isSameSequenceAndModificationStatus(Peptide anotherPeptide,
                                          AminoAcidPattern.MatchingType matchingType,
                                          Double massTolerance)

Indicates whether another peptide has the same sequence and modification status without accounting for modification localization.

Parameters:

anotherPeptide - the other peptide to compare to this instance

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

a boolean indicating whether the other peptide has the same sequence and modification status.

isSameSequence

public boolean isSameSequence(Peptide anotherPeptide,
                     AminoAcidPattern.MatchingType matchingType,
                     Double massTolerance)

Returns a boolean indicating whether another peptide has the same sequence as the given peptide

Parameters:

anotherPeptide - the other peptide to compare

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

a boolean indicating whether the other peptide has the same sequence

isSameModificationStatus

public boolean isSameModificationStatus(Peptide anotherPeptide)

Indicates whether another peptide has the same variable modifications as this peptide. The localization of the PTM is not accounted for.

Parameters:

anotherPeptide - the other peptide

Returns:

a boolean indicating whether the other peptide has the same variable modifications as the peptide of interest

sameModificationsAs

public boolean sameModificationsAs(Peptide anotherPeptide,
                          ArrayList<String> ptms)

Indicates whether another peptide has the same modifications at the same localization as this peptide. This method comes as a complement of isSameAs, here the localization of all PTMs is taken into account.

Parameters:

anotherPeptide - another peptide

ptms - the PTMs

Returns:

true if the other peptide has the same positions at the same location as the considered peptide

sameModificationsAs

public boolean sameModificationsAs(Peptide anotherPeptide)

Indicates whether another peptide has the same modifications at the same localization as this peptide. This method comes as a complement of isSameAs, here the localization of all PTMs is taken into account.

Parameters:

anotherPeptide - another peptide

Returns:

true if the other peptide has the same positions at the same location as the considered peptide

getNTerminal

public String getNTerminal()

Returns the N-terminal of the peptide as a String. Returns "NH2" if the terminal is not modified, otherwise returns the name of the modification. /!\ this method will work only if the PTM found in the peptide are in the PTMFactory.

Returns:

the N-terminal of the peptide as a String, e.g., "NH2"

getCTerminal

public String getCTerminal()

Returns the C-terminal of the peptide as a String. Returns "COOH" if the terminal is not modified, otherwise returns the name of the modification. /!\ This method will work only if the PTM found in the peptide are in the PTMFactory.

Returns:

the C-terminal of the peptide as a String, e.g., "COOH"

getTaggedModifiedSequence

public String getTaggedModifiedSequence(ModificationProfile modificationProfile,
                               boolean useHtmlColorCoding,
                               boolean includeHtmlStartEndTags,
                               boolean useShortName,
                               boolean excludeAllFixedPtms)

Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>. /!\ this method will work only if the PTM found in the peptide are in the PTMFactory. /!\ This method uses the modifications as set in the modification matches of this peptide and displays all of them.

Parameters:

modificationProfile - the modification profile of the search

useHtmlColorCoding - if true, color coded HTML is used, otherwise PTM tags, e.g, <mox>, are used

includeHtmlStartEndTags - if true, start and end HTML tags are added

useShortName - if true the short names are used in the tags

excludeAllFixedPtms - if true, all fixed PTMs are excluded

Returns:

the modified sequence as a tagged string

getTaggedModifiedSequence

public String getTaggedModifiedSequence(ModificationProfile modificationProfile,
                               boolean useHtmlColorCoding,
                               boolean includeHtmlStartEndTags,
                               boolean useShortName)

Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>. /!\ this method will work only if the PTM found in the peptide are in the PTMFactory. /!\ This method uses the modifications as set in the modification matches of this peptide and displays all of them.

Parameters:

modificationProfile - the modification profile of the search

useHtmlColorCoding - if true, color coded HTML is used, otherwise PTM tags, e.g, <mox>, are used

includeHtmlStartEndTags - if true, start and end HTML tags are added

useShortName - if true the short names are used in the tags

Returns:

the modified sequence as a tagged string

getTaggedModifiedSequence

public static String getTaggedModifiedSequence(ModificationProfile modificationProfile,
                               Peptide peptide,
                               HashMap<Integer,ArrayList<String>> mainModificationSites,
                               HashMap<Integer,ArrayList<String>> secondaryModificationSites,
                               HashMap<Integer,ArrayList<String>> fixedModificationSites,
                               boolean useHtmlColorCoding,
                               boolean includeHtmlStartEndTags,
                               boolean useShortName)

Returns the modified sequence as an tagged string with potential modification sites color coded or with PTM tags, e.g, <mox>. /!\ This method will work only if the PTM found in the peptide are in the PTMFactory. /!\ This method uses the modifications as set in the modification matches of this peptide and displays all of them.

Parameters:

modificationProfile - the modification profile of the search

includeHtmlStartEndTags - if true, start and end HTML tags are added

peptide - the peptide to annotate

mainModificationSites - the main variable modification sites in a map: aa number -> list of modifications (1 is the first AA) (can be null)

secondaryModificationSites - the secondary variable modification sites in a map: aa number -> list of modifications (1 is the first AA) (can be null)

fixedModificationSites - the fixed modification sites in a map: aa number -> list of modifications (1 is the first AA) (can be null)

useHtmlColorCoding - if true, color coded HTML is used, otherwise PTM tags, e.g, <mox>, are used

useShortName - if true the short names are used in the tags

Returns:

the tagged modified sequence as a string

getModifiedIndexes

public ArrayList<Integer> getModifiedIndexes()

Returns the indexes of the residues in the peptide that contain at least one variable modification.

Returns:

the indexes of the modified residues

getModifiedIndexes

public ArrayList<Integer> getModifiedIndexes(boolean excludeFixed)

Returns the indexes of the residues in the peptide that contain at least one modification.

Parameters:

excludeFixed - exclude fixed PTMs

Returns:

the indexes of the modified residues

getIndexedFixedModifications

public HashMap<Integer,ArrayList<String>> getIndexedFixedModifications()

Returns an indexed map of all fixed modifications amino acid, (1 is the first) -> list of modification names.

Returns:

an indexed map of all fixed modifications amino acid

estimateTheoreticMass

public void estimateTheoreticMass()
                           throws IllegalArgumentException

Estimates the theoretic mass of the peptide. The previous version is silently overwritten.

Throws:

IllegalArgumentException - if the peptide sequence contains unknown amino acids

isNterm

public ArrayList<String> isNterm(AminoAcidPattern.MatchingType matchingType,
                        Double massTolerance)
                          throws IOException,
                                 IllegalArgumentException,
                                 InterruptedException,
                                 FileNotFoundException,
                                 ClassNotFoundException,
                                 SQLException

Returns a list of proteins where this peptide can be found in the N-terminus. The proteins must be accessible via the sequence factory. If none found, an empty list is returned. Warning: if the parent proteins are not set, they will be set using the default protein tree and the given matching type and mass tolerance

Parameters:

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

a list of proteins where this peptide can be found in the N-terminus

Throws:

IOException - exception thrown whenever an error occurred while reading the protein sequence

IllegalArgumentException - exception thrown whenever an error occurred while reading the protein sequence

InterruptedException - exception thrown whenever an error occurred while reading the protein sequence

FileNotFoundException

ClassNotFoundException

SQLException

isCterm

public ArrayList<String> isCterm(AminoAcidPattern.MatchingType matchingType,
                        Double massTolerance)
                          throws IOException,
                                 IllegalArgumentException,
                                 InterruptedException,
                                 FileNotFoundException,
                                 ClassNotFoundException,
                                 SQLException

Returns a list of proteins where this peptide can be found in the C-terminus. The proteins must be accessible via the sequence factory. If none found, an empty list is returned. Warning: if the parent proteins are not set, they will be set using the default protein tree and the given matching type and mass tolerance

Parameters:

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

a list of proteins where this peptide can be found in the C-terminus

Throws:

IOException - exception thrown whenever an error occurred while reading a protein sequence

IllegalArgumentException - exception thrown whenever an error occurred while reading a protein sequence

InterruptedException - exception thrown whenever an error occurred while reading a protein sequence

FileNotFoundException

ClassNotFoundException

SQLException

getSequenceAsPattern

public AminoAcidPattern getSequenceAsPattern()

Returns the sequence of this peptide as AminoAcidPattern.

Returns:

the sequence of this peptide as AminoAcidPattern

getSequenceAsPattern

public static AminoAcidPattern getSequenceAsPattern(String sequence)

Returns the given sequence as AminoAcidPattern.

Parameters:

sequence - the sequence of interest

Returns:

the sequence as AminoAcidPattern

isDecoy

public boolean isDecoy(AminoAcidPattern.MatchingType matchingType,
              Double massTolerance)
                throws IOException,
                       InterruptedException,
                       SQLException,
                       ClassNotFoundException

Indicates whether a peptide can be derived from a decoy protein.

Parameters:

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

whether a peptide can be derived from a decoy protein

Throws:

IOException

InterruptedException

SQLException

ClassNotFoundException

getNoModPeptide

public static Peptide getNoModPeptide(Peptide peptide,
                      ArrayList<PTM> ptms)
                               throws IOException,
                                      SQLException,
                                      ClassNotFoundException,
                                      InterruptedException

Returns a version of the peptide which does not contain the inspected PTMs.

Parameters:

peptide - the original peptide

ptms - list of inspected PTMs

Returns:

a not modified version of the peptide

Throws:

IOException

ClassNotFoundException

InterruptedException

SQLException