com.compomics.util.experiment.biology

Class PTMFactory

java.lang.Object

com.compomics.util.experiment.biology.PTMFactory

All Implemented Interfaces:

java.io.Serializable

public class PTMFactory
extends java.lang.Object
implements java.io.Serializable

This factory will load PTM from an XML file and provide them on demand as standard class.

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
boolean	defaultModsSorted Set to true if the default mods are sorted alphabetically.
static java.lang.String	SEARCH_SUFFIX Suffix for the modifications searched but not in the factory.
static PTM	unknownPTM Unknown modification to be returned when the modification is not found.
boolean	usersModsSorted Set to true if the users mods are sorted alphabetically.

Method Summary

Methods

Modifier and Type	Method and Description
void	addUserPTM(PTM ptm) Adds a new user modification.
void	checkFixedModifications(ModificationProfile modificationProfile, Peptide peptide, AminoAcidPattern.MatchingType matchingType, java.lang.Double massTolerance) Removes the fixed modifications of the peptide and remaps the one searched for according to the ModificationProfile.
void	clearFactory() Clears the factory getInstance() needs to be called afterwards.
boolean	containsPTM(java.lang.String name) Returns a boolean indicating whether the PTM is loaded in the factory.
java.lang.String	convertPridePtm(java.lang.String pridePtmName, ModificationProfile modProfile, java.util.ArrayList<java.lang.String> unknownPtms, boolean isFixed) Tries to convert a PRIDE PTM to utilities PTM name, and add it to the modification profile.
java.awt.Color	getColor(java.lang.String modification) Returns the color used to code the given modification.
static java.awt.Color	getDefaultColor(java.lang.String modification) Returns a default color based on the modification name.
java.util.ArrayList<java.lang.String>	getDefaultModifications() Returns the names of the default modifications.
java.util.ArrayList<java.lang.String>	getDefaultModificationsOrdered() Returns the alphabetically ordered names of the default modifications.
java.lang.Integer	getDefaultOMSSAIndex(java.lang.String modificationName) Returns the default OMSSA index of the modification.
static java.lang.String	getDefaultShortName(java.lang.String modificationName) Returns a default short name for a given modification.
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>>	getExpectedPTMs(ModificationProfile modificationProfile, Peptide peptide, double modificationMass, double massTolerance, AminoAcidPattern.MatchingType matchingType) Returns the expected modifications based on the modification profile, the peptide found and the modification details.
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>>	getExpectedPTMs(ModificationProfile modificationProfile, Peptide peptide, java.lang.String ptmName, AminoAcidPattern.MatchingType matchingType, java.lang.Double massTolerance) Returns the names of the possibly expected modification based on the name of the expected modification in a map where the PTM names are indexed by their potential site on the sequence.
static PTMFactory	getInstance() Static method to get the instance of the factory.
static java.util.HashMap<java.lang.String,java.lang.Integer>	getOMSSAIndexes(java.io.File modificationsFile) Imports the OMSSA indexes from an XML file.
java.lang.String	getOmssaUserModBloc(java.lang.String ptmName, int cpt) Returns an MSModSpec bloc as present in the OMSSA user modification files for a given PTM.
PTM	getPTM(double mass, java.lang.String location, java.lang.String sequence) Deprecated. This method can generate inconsistent results in case a measurement matches to various PTMs.
PTM	getPTM(ModificationProfile modificationProfile, int index) Get a PTM according to its OMSSA index.
PTM	getPTM(java.lang.String name) Returns the PTM indexed by its name.
java.util.ArrayList<java.lang.String>	getPTMs() Returns the names of all imported PTMs.
PTM	getSearchedPTM(PTM modification) Returns the standard search compatible PTM corresponding to this pattern.
PTM	getSearchedPTM(java.lang.String modificationName) Returns the standard search compatible PTM corresponding to this pattern, i.e., a pattern targeting a single amino acid and not a complex pattern.
java.lang.String	getShortName(java.lang.String modification) Returns the user favorite short name, a default short name otherwise.
java.util.ArrayList<java.lang.String>	getUserModifications() Returns the names of the user defined modifications.
java.util.ArrayList<java.lang.String>	getUserModificationsOrdered() Returns the alphabetically ordered names of the user defined modifications.
void	importModifications(java.io.File modificationsFile, boolean userMod) Import modifications from a modification file.
void	importModifications(java.io.File modificationsFile, boolean userMod, boolean overwrite) Import modifications from a modification file.
boolean	isUserDefined(java.lang.String ptmName) Convenience method returning a boolean indicating whether a PTM is user defined or default.
java.util.ArrayList<java.lang.String>	loadBackedUpModifications(SearchParameters searchParameters, boolean overwrite) Verifies that the modifications backed-up in the search parameters are loaded and alerts the user in case conflicts are found.
void	reloadFactory() Reloads the factory getInstance() needs to be called afterwards.
void	removeUserPtm(java.lang.String ptmName) Removes a user PTM.
void	saveFactory() Saves the factory in the user folder.
void	setColor(java.lang.String expectedModification, java.awt.Color color) Sets a new color for the given expected modification.
void	setDefaultNeutralLosses() Sets the default neutral losses of PTMs when not implemented.
void	setDefaultReporterIons() Sets the default reporter ions of PTMs when not implemented.
void	setSearchedOMSSAIndexes(ModificationProfile modificationProfile) Set the OMSSA indexes used for this search.
void	setShortName(java.lang.String modification, java.lang.String shortName) Sets the short name for a modification.
void	writeOmssaModificationsFiles(java.io.File aFolder, java.io.File utilitiesModFile, java.io.File utilitiesUserModFile) Write the OMSSA modification files to the given folder.
void	writeOmssaUserModificationFile(java.io.File file) Writes the OMSSA modification file corresponding to the PTMs loaded in the factory in the given file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

unknownPTM

public static final PTM unknownPTM

Unknown modification to be returned when the modification is not found.

SEARCH_SUFFIX

public static final java.lang.String SEARCH_SUFFIX

Suffix for the modifications searched but not in the factory.

See Also:

Constant Field Values

defaultModsSorted

public boolean defaultModsSorted

Set to true if the default mods are sorted alphabetically.

usersModsSorted

public boolean usersModsSorted

Set to true if the users mods are sorted alphabetically.

Method Detail

getInstance

public static PTMFactory getInstance()

Static method to get the instance of the factory.

Returns:

the instance of the factory

clearFactory

public void clearFactory()

Clears the factory getInstance() needs to be called afterwards.

reloadFactory

public void reloadFactory()

Reloads the factory getInstance() needs to be called afterwards.

saveFactory

public void saveFactory()
                 throws java.io.IOException

Saves the factory in the user folder.

Throws:

java.io.IOException - exception thrown whenever an error occurred while saving the ptmFactory

getPTM

public PTM getPTM(ModificationProfile modificationProfile,
         int index)

Get a PTM according to its OMSSA index.

Parameters:

index - the PTM index

modificationProfile - the modification profile used for the search

Returns:

the selected PTM

getSearchedPTM

public PTM getSearchedPTM(PTM modification)

Returns the standard search compatible PTM corresponding to this pattern. i.e. a pattern targeting a single amino acid and not a complex pattern.

Parameters:

modification - the modification of interest

Returns:

a search compatible modification

getSearchedPTM

public PTM getSearchedPTM(java.lang.String modificationName)

Returns the standard search compatible PTM corresponding to this pattern, i.e., a pattern targeting a single amino acid and not a complex pattern.

Parameters:

modificationName - the name of the modification of interest

Returns:

a search compatible modification

addUserPTM

public void addUserPTM(PTM ptm)

Adds a new user modification.

Parameters:

ptm - the new modification to add

removeUserPtm

public void removeUserPtm(java.lang.String ptmName)

Removes a user PTM.

Parameters:

ptmName - the name of the PTM to remove

getPTM

public PTM getPTM(java.lang.String name)

Returns the PTM indexed by its name.

Parameters:

name - the name of the desired PTM

Returns:

The desired PTM

containsPTM

public boolean containsPTM(java.lang.String name)

Returns a boolean indicating whether the PTM is loaded in the factory.

Parameters:

name - the name of the PTM

Returns:

a boolean indicating whether the PTM is loaded in the factory

getPTM

public PTM getPTM(double mass,
         java.lang.String location,
         java.lang.String sequence)

Deprecated. This method can generate inconsistent results in case a measurement matches to various PTMs.

Getter for a PTM according to its measured characteristics.

Parameters:

mass - the measured mass induced by the modification

location - the modification location

sequence - the peptide sequence

Returns:

the candidate modification, null if none is found

importModifications

public void importModifications(java.io.File modificationsFile,
                       boolean userMod)
                         throws org.xmlpull.v1.XmlPullParserException,
                                java.io.IOException

Import modifications from a modification file.

Parameters:

modificationsFile - A file containing modifications

userMod - A boolean indicating whether the file comprises user designed modification

Throws:

org.xmlpull.v1.XmlPullParserException - exception thrown whenever an error is encountered while parsing

java.io.IOException - exception thrown whenever an error is encountered reading the file

importModifications

public void importModifications(java.io.File modificationsFile,
                       boolean userMod,
                       boolean overwrite)
                         throws org.xmlpull.v1.XmlPullParserException,
                                java.io.IOException

Import modifications from a modification file.

Parameters:

modificationsFile - A file containing modifications

userMod - A boolean indicating whether the file comprises user designed modification

overwrite - a boolean indicating whether modifications from the XML file should be overwritten

Throws:

org.xmlpull.v1.XmlPullParserException - exception thrown whenever an error is encountered while parsing

java.io.IOException - exception thrown whenever an error is encountered reading the file

getDefaultOMSSAIndex

public java.lang.Integer getDefaultOMSSAIndex(java.lang.String modificationName)

Returns the default OMSSA index of the modification. Null if not found.

Parameters:

modificationName - the name of the modification

Returns:

the default OMSSA index

getOMSSAIndexes

public static java.util.HashMap<java.lang.String,java.lang.Integer> getOMSSAIndexes(java.io.File modificationsFile)
                                                                             throws org.xmlpull.v1.XmlPullParserException,
                                                                                    java.io.FileNotFoundException,
                                                                                    java.io.IOException

Imports the OMSSA indexes from an XML file.

Parameters:

modificationsFile - the modification file

Returns:

a map of all indexes: modification name -> OMSSA index

Throws:

org.xmlpull.v1.XmlPullParserException

java.io.FileNotFoundException

java.io.IOException

writeOmssaModificationsFiles

public void writeOmssaModificationsFiles(java.io.File aFolder,
                                java.io.File utilitiesModFile,
                                java.io.File utilitiesUserModFile)
                                  throws java.io.IOException

Write the OMSSA modification files to the given folder.

Parameters:

aFolder - the folder to write the modification files to

utilitiesModFile - the utilities corresponding mod file

utilitiesUserModFile - the utilities corresponding usermod file

Throws:

java.io.IOException - an IOException is thrown in case an issue is encountered while reading or writing a file.

writeOmssaUserModificationFile

public void writeOmssaUserModificationFile(java.io.File file)
                                    throws java.io.IOException

Writes the OMSSA modification file corresponding to the PTMs loaded in the factory in the given file.

Parameters:

file - the file

Throws:

java.io.IOException - exception thrown whenever an error occurred while writing the file

getOmssaUserModBloc

public java.lang.String getOmssaUserModBloc(java.lang.String ptmName,
                                   int cpt)

Returns an MSModSpec bloc as present in the OMSSA user modification files for a given PTM. Only the amino acids targeted by the pattern of the PTM will be considered.

Parameters:

ptmName - the name of the PTM

cpt - the index of this PTM

Returns:

a string containing the XML bloc

getDefaultModifications

public java.util.ArrayList<java.lang.String> getDefaultModifications()

Returns the names of the default modifications.

Returns:

the names of the default modifications

getDefaultModificationsOrdered

public java.util.ArrayList<java.lang.String> getDefaultModificationsOrdered()

Returns the alphabetically ordered names of the default modifications.

Returns:

the alphabetically ordered names of the default modifications

getUserModifications

public java.util.ArrayList<java.lang.String> getUserModifications()

Returns the names of the user defined modifications.

Returns:

the names of the user defined modifications

getUserModificationsOrdered

public java.util.ArrayList<java.lang.String> getUserModificationsOrdered()

Returns the alphabetically ordered names of the user defined modifications.

Returns:

the alphabetically ordered names of the user defined modifications

getPTMs

public java.util.ArrayList<java.lang.String> getPTMs()

Returns the names of all imported PTMs.

Returns:

the names of all imported PTMs

isUserDefined

public boolean isUserDefined(java.lang.String ptmName)

Convenience method returning a boolean indicating whether a PTM is user defined or default.

Parameters:

ptmName -

Returns:

boolean indicating whether a PTM is user defined

loadBackedUpModifications

public java.util.ArrayList<java.lang.String> loadBackedUpModifications(SearchParameters searchParameters,
                                                              boolean overwrite)

Verifies that the modifications backed-up in the search parameters are loaded and alerts the user in case conflicts are found.

Parameters:

searchParameters - the search parameters to load

overwrite - if true, overwrite the modification

Returns:

returns a list of modifications already loaded which should be checked.

getExpectedPTMs

public java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> getExpectedPTMs(ModificationProfile modificationProfile,
                                                                                         Peptide peptide,
                                                                                         double modificationMass,
                                                                                         double massTolerance,
                                                                                         AminoAcidPattern.MatchingType matchingType)
                                                                                           throws java.io.IOException,
                                                                                                  java.lang.IllegalArgumentException,
                                                                                                  java.lang.InterruptedException,
                                                                                                  java.io.FileNotFoundException,
                                                                                                  java.lang.ClassNotFoundException,
                                                                                                  java.io.FileNotFoundException,
                                                                                                  java.sql.SQLException

Returns the expected modifications based on the modification profile, the peptide found and the modification details. Returns the names in a map where the modification names are indexed by the index on the sequence. 1 is the first amino acid.

Parameters:

modificationProfile - the modification profile used for the search (available in the search parameters)

peptide - the peptide identified with the parent proteins (necessary for protein termini modifications)

modificationMass - the modification mass as found in the search results

massTolerance - the mass tolerance to use to match the modification mass

matchingType - the type of sequence matching

Returns:

a map of expected PTMs corresponding to the given characteristics. Empty if none found.

Throws:

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

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

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

java.io.FileNotFoundException

java.lang.ClassNotFoundException

java.sql.SQLException

getExpectedPTMs

public java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> getExpectedPTMs(ModificationProfile modificationProfile,
                                                                                         Peptide peptide,
                                                                                         java.lang.String ptmName,
                                                                                         AminoAcidPattern.MatchingType matchingType,
                                                                                         java.lang.Double massTolerance)
                                                                                           throws java.io.IOException,
                                                                                                  java.lang.IllegalArgumentException,
                                                                                                  java.lang.InterruptedException,
                                                                                                  java.io.FileNotFoundException,
                                                                                                  java.lang.ClassNotFoundException,
                                                                                                  java.sql.SQLException

Returns the names of the possibly expected modification based on the name of the expected modification in a map where the PTM names are indexed by their potential site on the sequence. 1 is the first amino acid. Candidate PTMs are expected non fixed modifications with the same mass.

Parameters:

modificationProfile - the modification profile used for the search (available in the search parameters)

peptide - the peptide

ptmName - the name of the searched PTM

matchingType - the matching type

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

Returns:

the possible expected modification names. Empty if not found.

Throws:

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

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

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

java.io.FileNotFoundException

java.lang.ClassNotFoundException

java.sql.SQLException

checkFixedModifications

public void checkFixedModifications(ModificationProfile modificationProfile,
                           Peptide peptide,
                           AminoAcidPattern.MatchingType matchingType,
                           java.lang.Double massTolerance)
                             throws java.io.IOException,
                                    java.lang.IllegalArgumentException,
                                    java.lang.InterruptedException,
                                    java.io.FileNotFoundException,
                                    java.lang.ClassNotFoundException,
                                    java.sql.SQLException

Removes the fixed modifications of the peptide and remaps the one searched for according to the ModificationProfile. Note: for protein terminal modification the protein must be loaded in the sequence factory.

Parameters:

modificationProfile -

peptide - the peptide

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise. (Only useful when considering modifications targeting a motif comprising interchangeable amino acids, e.g., glyco)

Throws:

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

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

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

java.io.FileNotFoundException

java.lang.ClassNotFoundException

java.sql.SQLException

setSearchedOMSSAIndexes

public void setSearchedOMSSAIndexes(ModificationProfile modificationProfile)

Set the OMSSA indexes used for this search.

Parameters:

modificationProfile - the modification profile of this search

setDefaultNeutralLosses

public void setDefaultNeutralLosses()

Sets the default neutral losses of PTMs when not implemented.

setDefaultReporterIons

public void setDefaultReporterIons()

Sets the default reporter ions of PTMs when not implemented.

setShortName

public void setShortName(java.lang.String modification,
                java.lang.String shortName)

Sets the short name for a modification.

Parameters:

modification - the modification name

shortName - the short name

getShortName

public java.lang.String getShortName(java.lang.String modification)

Returns the user favorite short name, a default short name otherwise.

Parameters:

modification - the name of the modification

Returns:

the corresponding short name

getDefaultShortName

public static java.lang.String getDefaultShortName(java.lang.String modificationName)

Returns a default short name for a given modification.

Parameters:

modificationName - the full name of the modification

Returns:

the default short name

getColor

public java.awt.Color getColor(java.lang.String modification)

Returns the color used to code the given modification.

Parameters:

modification - the name of the given expected modification

Returns:

the corresponding color

setColor

public void setColor(java.lang.String expectedModification,
            java.awt.Color color)

Sets a new color for the given expected modification.

Parameters:

expectedModification - the name of the expected modification

color - the new color

getDefaultColor

public static java.awt.Color getDefaultColor(java.lang.String modification)

Returns a default color based on the modification name.

Parameters:

modification - the name of the modification

Returns:

a default color.

convertPridePtm

public java.lang.String convertPridePtm(java.lang.String pridePtmName,
                               ModificationProfile modProfile,
                               java.util.ArrayList<java.lang.String> unknownPtms,
                               boolean isFixed)

Tries to convert a PRIDE PTM to utilities PTM name, and add it to the modification profile. Unknown PTMs are added to the unknown PTMs arraylist.

Parameters:

pridePtmName - the PRIDE PTM name

modProfile - the modification profile to add the PTMs to

unknownPtms - the list of unknown PTMS, updated during this method

isFixed - if true, the PTM will be added as a fixed modification

Returns:

a pride parameters report as a string (for use in PRIDE Reshake)