org.fhcrc.cpl.toolbox.proteomics
Class ProteinUtilities

java.lang.Object
  org.fhcrc.cpl.toolbox.proteomics.ProteinUtilities

public class ProteinUtilities
extends java.lang.Object

This class doesn't do parsing of ProtXML files itself. It uses ProtXmlReader for that. This is for utilities to work with the output of ProtXmlReader

Field Summary

protected static org.apache.log4j.Logger

_log

Constructor Summary

ProteinUtilities()

Method Summary

static void	assignContainingProteinsToFeatures(Feature[] ms1FeaturesWithPeptides, java.io.File fastaFile)
static void	createPepXml(Feature[] featuresWithPeptides, java.io.File fastaFile, java.io.File outputFile) Create a pepxml file that can be used with proteinprophet
static java.util.Map<java.lang.String,java.util.Set<java.lang.String>>	findFastaProteinsForPeptides(java.util.Collection<java.lang.String> peptideList, java.io.File fastaFile)
static java.util.List<java.io.File>	findSourcePepXMLFiles(java.io.File protXmlFile) Look inside a protXML file to find the source PepXML files
static PanelWithChart	generateSensSpecChart(java.io.File protXmlFile) Generate a sensitivity-and-specificity-curve chart
static PanelWithChart	generateSensSpecChart(java.io.File protXmlFile1, java.io.File protXmlFile2) Generate a sensitivity-and-specificity-curve chart for two files.
protected static Pair<java.lang.Character,java.lang.Character>	getPrevNextAAs(java.lang.String peptide, Protein protein)
static void	guessAllProteinsForFeaturePeptides(FeatureSet[] featureSets, java.io.File fastaFile, Protein[] fastaProteins) For every feature with a peptide in every featureset passed in, find ALL proteins in the fasta file that contains that peptide, and assign them all.
static void	guessProteinsForFeaturePeptides(FeatureSet[] featureSets, java.io.File fastaFile) cover method
static void	guessProteinsForFeaturePeptides(FeatureSet[] featureSets, java.io.File fastaFile, Protein[] fastaProteins) For every feature with a peptide in every featureset passed in, find some protein in the fasta file that contains that peptide, and assign it
static void	guessProteinsForFeaturePeptides(FeatureSet featureSet, java.io.File fastaFile) helper method for one featureset
static void	guessProteinsForFeaturePeptides(FeatureSet featureSet, Protein[] fastaProteins) helper method for one featureset
static java.util.Map<java.lang.String,ProtXmlReader.Protein>	loadFirstProteinOccurrence(java.io.File protXmlFile, java.util.Collection<java.lang.String> proteinNames, float minProteinProphetGroupProbability) Returns a map from protein names to first occurrences of proteins in the protXML file, if they exist with minimum probability
static ProtXmlReader.Protein	loadFirstProteinOccurrence(java.io.File protXmlFile, java.lang.String proteinName) returns null if protein not found
static ProtXmlReader.Protein	loadFirstProteinOccurrence(java.io.File protXmlFile, java.lang.String proteinName, float minProteinProphetGroupProbability) returns null if protein not found with a minimum group probability
static java.util.Map<java.lang.String,java.util.Set<java.lang.Integer>>	loadPeptideProteinGroupMapFromProtXML(java.io.File protXmlFile, double minProteinProphet) Create a mapping between all peptides noted in the protXml file, and all protein groups that they are associated with.
static java.util.Map<java.lang.String,java.util.Set<java.lang.String>>	loadPeptideProteinMapFromProtXML(java.io.File protXmlFile, double minProteinProphet) Create a mapping between all peptides noted in the protXml file, and all proteins that they are associated with.
static java.util.List<ProteinGroup>	loadProteinGroupsFromProtXML(java.io.File protXmlFile) WARNING! after running through the iterator, the proteins in each group disappear
static java.util.Map<java.lang.String,java.util.List<ProtXmlReader.Peptide>>	loadProteinPeptideMapFromProtXML(java.io.File protXmlFile, double minProteinProphet) Create a mapping between all proteins in the protxml file, and all peptides associated with them.
static java.util.Map<java.lang.String,java.util.Set<java.lang.String>>	loadProteinPeptideSequenceMapFromProtXML(java.io.File protXmlFile, double minProteinProphet) Create a mapping between all proteins in the protxml file, and all peptides associated with them.
static java.util.Map<java.lang.String,java.lang.Float>	loadProteinProbabilityMapFromProtXML(java.io.File protXmlFile) Create a mapping between all proteins in the protxml file, and all peptides associated with them.
static java.util.ArrayList<Protein>	loadProteinsFromFasta(java.io.File fastaFile) Load all proteins from a fasta file
static java.util.List<ProtXmlReader.Protein>	loadProtXmlProteinsFromProtXML(java.io.File protXmlFile)
static java.util.Set<java.lang.String>	loadTrypticPeptidesFromFasta(java.io.File fastaFile)
static java.util.Map<java.lang.String,java.util.List<Protein>>	mapPeptidesToProteins(java.util.Set<java.lang.String> peptides, java.io.File[] protXmlFiles, Protein[] proteinsInFasta, double minProteinProphet) Map peptides to proteins using multiple protxml files
static java.util.Map<java.lang.String,java.util.List<Protein>>	mapPeptidesToProteins(java.util.Set<java.lang.String> peptides, java.io.File protXmlFile, Protein[] proteinsInFasta, double minProteinProphet) Map peptides to proteins.

Methods inherited from class java.lang.Object

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

Field Detail

_log

protected static org.apache.log4j.Logger _log

Constructor Detail

ProteinUtilities

public ProteinUtilities()

Method Detail

loadPeptideProteinMapFromProtXML

public static java.util.Map<java.lang.String,java.util.Set<java.lang.String>> loadPeptideProteinMapFromProtXML(java.io.File protXmlFile,
                                                                                                               double minProteinProphet)
                                                                                                        throws java.io.FileNotFoundException,
                                                                                                               javax.xml.stream.XMLStreamException

Create a mapping between all peptides noted in the protXml file, and all proteins that they are associated with. This means all indistinguishable proteins

Parameters:

protXmlFile -

Returns:

Throws:

CommandLineModuleExecutionException

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

findSourcePepXMLFiles

public static java.util.List<java.io.File> findSourcePepXMLFiles(java.io.File protXmlFile)
                                                          throws java.io.FileNotFoundException,
                                                                 javax.xml.stream.XMLStreamException

Look inside a protXML file to find the source PepXML files

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

generateSensSpecChart

public static PanelWithChart generateSensSpecChart(java.io.File protXmlFile)
                                            throws java.io.FileNotFoundException,
                                                   javax.xml.stream.XMLStreamException

Generate a sensitivity-and-specificity-curve chart

Parameters:

protXmlFile -

Returns:

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

generateSensSpecChart

public static PanelWithChart generateSensSpecChart(java.io.File protXmlFile1,
                                                   java.io.File protXmlFile2)
                                            throws java.io.FileNotFoundException,
                                                   javax.xml.stream.XMLStreamException

Generate a sensitivity-and-specificity-curve chart for two files. Second one will have dashed lines

Parameters:

protXmlFile1 -

protXmlFile2 -

Returns:

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

loadPeptideProteinGroupMapFromProtXML

public static java.util.Map<java.lang.String,java.util.Set<java.lang.Integer>> loadPeptideProteinGroupMapFromProtXML(java.io.File protXmlFile,
                                                                                                                     double minProteinProphet)
                                                                                                              throws java.io.FileNotFoundException,
                                                                                                                     javax.xml.stream.XMLStreamException

Create a mapping between all peptides noted in the protXml file, and all protein groups that they are associated with.

Parameters:

protXmlFile -

Returns:

Throws:

CommandLineModuleExecutionException

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

loadProteinPeptideMapFromProtXML

public static java.util.Map<java.lang.String,java.util.List<ProtXmlReader.Peptide>> loadProteinPeptideMapFromProtXML(java.io.File protXmlFile,
                                                                                                                     double minProteinProphet)
                                                                                                              throws java.io.FileNotFoundException,
                                                                                                                     javax.xml.stream.XMLStreamException

Create a mapping between all proteins in the protxml file, and all peptides associated with them. This means all indistinguishable proteins

Parameters:

protXmlFile -

Returns:

Throws:

CommandLineModuleExecutionException

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

loadProteinPeptideSequenceMapFromProtXML

public static java.util.Map<java.lang.String,java.util.Set<java.lang.String>> loadProteinPeptideSequenceMapFromProtXML(java.io.File protXmlFile,
                                                                                                                       double minProteinProphet)
                                                                                                                throws java.io.FileNotFoundException,
                                                                                                                       javax.xml.stream.XMLStreamException

Create a mapping between all proteins in the protxml file, and all peptides associated with them. This means all indistinguishable proteins

Parameters:

protXmlFile -

Returns:

Throws:

CommandLineModuleExecutionException

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

loadProteinProbabilityMapFromProtXML

public static java.util.Map<java.lang.String,java.lang.Float> loadProteinProbabilityMapFromProtXML(java.io.File protXmlFile)
                                                                                            throws java.io.FileNotFoundException,
                                                                                                   javax.xml.stream.XMLStreamException

Create a mapping between all proteins in the protxml file, and all peptides associated with them. This means all indistinguishable proteins

Parameters:

protXmlFile -

Returns:

Throws:

CommandLineModuleExecutionException

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

loadProteinGroupsFromProtXML

public static java.util.List<ProteinGroup> loadProteinGroupsFromProtXML(java.io.File protXmlFile)
                                                                 throws java.io.FileNotFoundException,
                                                                        javax.xml.stream.XMLStreamException

WARNING! after running through the iterator, the proteins in each group disappear

Parameters:

protXmlFile -

Returns:

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

loadProtXmlProteinsFromProtXML

public static java.util.List<ProtXmlReader.Protein> loadProtXmlProteinsFromProtXML(java.io.File protXmlFile)
                                                                            throws java.io.FileNotFoundException,
                                                                                   javax.xml.stream.XMLStreamException

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

loadFirstProteinOccurrence

public static ProtXmlReader.Protein loadFirstProteinOccurrence(java.io.File protXmlFile,
                                                               java.lang.String proteinName,
                                                               float minProteinProphetGroupProbability)
                                                        throws java.io.FileNotFoundException,
                                                               javax.xml.stream.XMLStreamException

returns null if protein not found with a minimum group probability

Parameters:

protXmlFile -

proteinName -

minProteinProphetGroupProbability -

Returns:

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

loadFirstProteinOccurrence

public static ProtXmlReader.Protein loadFirstProteinOccurrence(java.io.File protXmlFile,
                                                               java.lang.String proteinName)
                                                        throws java.io.FileNotFoundException,
                                                               javax.xml.stream.XMLStreamException

returns null if protein not found

Parameters:

protXmlFile -

proteinName -

Returns:

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

loadFirstProteinOccurrence

public static java.util.Map<java.lang.String,ProtXmlReader.Protein> loadFirstProteinOccurrence(java.io.File protXmlFile,
                                                                                               java.util.Collection<java.lang.String> proteinNames,
                                                                                               float minProteinProphetGroupProbability)
                                                                                        throws java.io.FileNotFoundException,
                                                                                               javax.xml.stream.XMLStreamException

Returns a map from protein names to first occurrences of proteins in the protXML file, if they exist with minimum probability

Parameters:

protXmlFile -

proteinNames -

minProteinProphetGroupProbability -

Returns:

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

createPepXml

public static void createPepXml(Feature[] featuresWithPeptides,
                                java.io.File fastaFile,
                                java.io.File outputFile)
                         throws CommandLineModuleExecutionException

Create a pepxml file that can be used with proteinprophet

Throws:

CommandLineModuleExecutionException

loadProteinsFromFasta

public static java.util.ArrayList<Protein> loadProteinsFromFasta(java.io.File fastaFile)

Load all proteins from a fasta file

Parameters:

fastaFile -

Returns:

loadTrypticPeptidesFromFasta

public static java.util.Set<java.lang.String> loadTrypticPeptidesFromFasta(java.io.File fastaFile)

findFastaProteinsForPeptides

public static java.util.Map<java.lang.String,java.util.Set<java.lang.String>> findFastaProteinsForPeptides(java.util.Collection<java.lang.String> peptideList,
                                                                                                           java.io.File fastaFile)

assignContainingProteinsToFeatures

public static void assignContainingProteinsToFeatures(Feature[] ms1FeaturesWithPeptides,
                                                      java.io.File fastaFile)

Parameters:

ms1FeaturesWithPeptides -

fastaFile -

mapPeptidesToProteins

public static java.util.Map<java.lang.String,java.util.List<Protein>> mapPeptidesToProteins(java.util.Set<java.lang.String> peptides,
                                                                                            java.io.File[] protXmlFiles,
                                                                                            Protein[] proteinsInFasta,
                                                                                            double minProteinProphet)
                                                                                     throws java.io.FileNotFoundException,
                                                                                            javax.xml.stream.XMLStreamException

Map peptides to proteins using multiple protxml files

Parameters:

peptides -

protXmlFiles -

proteinsInFasta -

Returns:

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

mapPeptidesToProteins

public static java.util.Map<java.lang.String,java.util.List<Protein>> mapPeptidesToProteins(java.util.Set<java.lang.String> peptides,
                                                                                            java.io.File protXmlFile,
                                                                                            Protein[] proteinsInFasta,
                                                                                            double minProteinProphet)
                                                                                     throws java.io.FileNotFoundException,
                                                                                            javax.xml.stream.XMLStreamException

Map peptides to proteins. If the user has supplied a fasta file, do this based on sequence. If the user has supplied a protxml file, do this based on that. protxml file takes precedence

Parameters:

peptides -

Returns:

Throws:

java.io.FileNotFoundException

javax.xml.stream.XMLStreamException

guessProteinsForFeaturePeptides

public static void guessProteinsForFeaturePeptides(FeatureSet featureSet,
                                                   java.io.File fastaFile)

helper method for one featureset

Parameters:

featureSet -

fastaFile -

guessProteinsForFeaturePeptides

public static void guessProteinsForFeaturePeptides(FeatureSet featureSet,
                                                   Protein[] fastaProteins)

helper method for one featureset

Parameters:

featureSet -

fastaProteins -

guessProteinsForFeaturePeptides

public static void guessProteinsForFeaturePeptides(FeatureSet[] featureSets,
                                                   java.io.File fastaFile)

cover method

Parameters:

featureSets -

fastaFile -

guessProteinsForFeaturePeptides

public static void guessProteinsForFeaturePeptides(FeatureSet[] featureSets,
                                                   java.io.File fastaFile,
                                                   Protein[] fastaProteins)

For every feature with a peptide in every featureset passed in, find some protein in the fasta file that contains that peptide, and assign it

Parameters:

featureSets -

fastaProteins -

guessAllProteinsForFeaturePeptides

public static void guessAllProteinsForFeaturePeptides(FeatureSet[] featureSets,
                                                      java.io.File fastaFile,
                                                      Protein[] fastaProteins)

For every feature with a peptide in every featureset passed in, find ALL proteins in the fasta file that contains that peptide, and assign them all. This is much more computationally intensive than finding just one

Parameters:

featureSets -

fastaProteins -

getPrevNextAAs

protected static Pair<java.lang.Character,java.lang.Character> getPrevNextAAs(java.lang.String peptide,
                                                                              Protein protein)