com.compomics.util.experiment.identification.protein_inference.proteintree

Class ProteinTree

java.lang.Object

com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree

public class ProteinTree
extends Object

This class sorts the proteins into groups.

Author:

Marc Vaudel

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	ProteinTree.PeptideIterator Alphabetical iterator for the tree.

Field Summary

Fields

Modifier and Type	Field and Description
static int	proteinBatchSize The number of proteins which should be imported at a time.
static String	version The version of the protein tree.

Constructor Summary

Constructors

Constructor and Description
ProteinTree(int memoryAllocation, int cacheSize) Creates a tree based on the proteins present in the sequence factory.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes all connections to files.
boolean	deleteDb() Try to delete the current database.
void	emptyCache() Empties the cache.
int	getCacheSize() Returns the size of the cache used for peptide mappings (note that there are two of them).
HashMap<String,ArrayList<Integer>>	getMatchedPeptideSequences(String peptideSequence, String proteinAccession, AminoAcidPattern.MatchingType matchingType, Double massTolerance, boolean limitXs) Returns a list of peptides matched using the given peptide sequence in the given protein according the provided matching settings.
int	getMemoryAllocation() Returns the memory allocation.
int	getNodesInCache() Returns the number of nodes currently loaded in cache.
ProteinTree.PeptideIterator	getPeptideIterator() Returns a PeptideIterator which iterates alphabetically all peptides corresponding to the end of a branch in the tree.
Integer	getProteinLength(String accession) Retrieves the length of a protein.
HashMap<String,ArrayList<Integer>>	getProteinMapping(String peptideSequence) Returns the protein mapping in the sequence factory for the given peptide sequence based on string matching only.
HashMap<String,HashMap<String,ArrayList<Integer>>>	getProteinMapping(String peptideSequence, AminoAcidPattern.MatchingType matchingType, Double massTolerance, boolean limitXs) Returns the protein mapping in the sequence factory for the given peptide sequence.
HashMap<Peptide,HashMap<String,ArrayList<Integer>>>	getProteinMapping(Tag tag, AminoAcidPattern.MatchingType matchingType, Double massTolerance, ArrayList<String> fixedModifications, ArrayList<String> variableModifications, boolean limitXs, boolean reportFixedPtms) Returns the protein mappings for the given peptide sequence.
void	initiateTree(int initialTagSize, int maxNodeSize, int maxPeptideSize, Enzyme enzyme, WaitingHandler waitingHandler, boolean printExpectedImportTime, boolean displayProgress) Initiates the tree.
void	initiateTree(int initialTagSize, int maxNodeSize, int maxPeptideSize, WaitingHandler waitingHandler, boolean printExpectedImportTime, boolean displayProgress) Initiates the tree.
void	reduceNodeCacheSize(double share) Reduces the node cache size by the given share.
void	setCacheSize(int cacheSize) Sets the size of the cache used for peptide mappings (note that there are two of them).
void	setMemoryAllocation(int memoryAllocation) Sets the memory allocation.

Methods inherited from class java.lang.Object

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

Field Detail

version

public static final String version

The version of the protein tree.

See Also:

Constant Field Values

proteinBatchSize

public static final int proteinBatchSize

The number of proteins which should be imported at a time.

See Also:

Constant Field Values

Constructor Detail

ProteinTree

public ProteinTree(int memoryAllocation,
           int cacheSize)
            throws IOException

Creates a tree based on the proteins present in the sequence factory.

Parameters:

memoryAllocation - the number of MB available for the tree in memory.

cacheSize - the peptide queries caches size (note, there are two of them)

Throws:

IOException

Method Detail

getMemoryAllocation

public int getMemoryAllocation()

Returns the memory allocation.

Returns:

the memory allocation

setMemoryAllocation

public void setMemoryAllocation(int memoryAllocation)

Sets the memory allocation.

Parameters:

memoryAllocation - the memory allocation

initiateTree

public void initiateTree(int initialTagSize,
                int maxNodeSize,
                int maxPeptideSize,
                WaitingHandler waitingHandler,
                boolean printExpectedImportTime,
                boolean displayProgress)
                  throws IOException,
                         IllegalArgumentException,
                         InterruptedException,
                         ClassNotFoundException,
                         SQLException

Initiates the tree.

Parameters:

initialTagSize - the initial tag size

maxNodeSize - the maximal size of a node. large nodes will be fast to initiate but slow to query. I typically use 500 giving an approximate query time <20ms.

maxPeptideSize - the maximum peptide size

waitingHandler - the waiting handler used to display progress to the user. Can be null but strongly recommended :)

printExpectedImportTime - if true the expected import time will be printed to the waiting handler

displayProgress - display progress

Throws:

IOException

IllegalArgumentException

InterruptedException

ClassNotFoundException

SQLException

initiateTree

public void initiateTree(int initialTagSize,
                int maxNodeSize,
                int maxPeptideSize,
                Enzyme enzyme,
                WaitingHandler waitingHandler,
                boolean printExpectedImportTime,
                boolean displayProgress)
                  throws IOException,
                         IllegalArgumentException,
                         InterruptedException,
                         IOException,
                         IllegalArgumentException,
                         InterruptedException,
                         ClassNotFoundException,
                         SQLException

Initiates the tree. Note: speed and memory are calibrated for the no enzyme case.

Parameters:

initialTagSize - the initial size of peptide tag. Large initial size are fast to query, low initial size are fast to initiate. I typically use 3 for databases containing less than 100 000 proteins giving an approximate initiation time of 60ms per accession.

maxNodeSize - the maximal size of a node. large nodes will be fast to initiate but slow to query. I typically use 500 giving an approximate query time <20ms.

maxPeptideSize - the maximum peptide size

enzyme - the enzyme used to select peptides. If null all possible peptides will be indexed

waitingHandler - the waiting handler used to display progress to the user. Can be null.

printExpectedImportTime - if true the expected import time will be printed to the waiting handler

displayProgress - display progress

Throws:

IOException

IllegalArgumentException

InterruptedException

ClassNotFoundException

SQLException

deleteDb

public boolean deleteDb()

Try to delete the current database.

Returns:

true of the deletion was a success

getProteinMapping

public HashMap<String,ArrayList<Integer>> getProteinMapping(String peptideSequence)
                                                     throws IOException,
                                                            InterruptedException,
                                                            ClassNotFoundException,
                                                            SQLException

Returns the protein mapping in the sequence factory for the given peptide sequence based on string matching only.

Parameters:

peptideSequence - the peptide sequence

Returns:

the peptide to protein mapping: Accession -> list of indexes where the peptide can be found on the sequence. An empty map if not found.

Throws:

IOException

InterruptedException

ClassNotFoundException

SQLException

getProteinMapping

public HashMap<String,HashMap<String,ArrayList<Integer>>> getProteinMapping(String peptideSequence,
                                                                   AminoAcidPattern.MatchingType matchingType,
                                                                   Double massTolerance,
                                                                   boolean limitXs)
                                                                     throws IOException,
                                                                            InterruptedException,
                                                                            ClassNotFoundException,
                                                                            SQLException

Returns the protein mapping in the sequence factory for the given peptide sequence.

Parameters:

peptideSequence - the peptide sequence

matchingType - the matching type

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

limitXs - if true the share of Xs in the peptide sequences will be limited in order to increase sequencing speed.

Returns:

the peptide to protein mapping: peptide sequence -> protein accession -> index in the protein An empty map if not

Throws:

IOException

InterruptedException

ClassNotFoundException

SQLException

getProteinMapping

public HashMap<Peptide,HashMap<String,ArrayList<Integer>>> getProteinMapping(Tag tag,
                                                                    AminoAcidPattern.MatchingType matchingType,
                                                                    Double massTolerance,
                                                                    ArrayList<String> fixedModifications,
                                                                    ArrayList<String> variableModifications,
                                                                    boolean limitXs,
                                                                    boolean reportFixedPtms)
                                                                      throws IOException,
                                                                             InterruptedException,
                                                                             ClassNotFoundException,
                                                                             SQLException

Returns the protein mappings for the given peptide sequence. peptide sequence -> protein accession -> index in the protein. An empty map if not found.

Parameters:

tag - the tag to look for in the tree. Must contain a consecutive amino acid sequence of longer or equal size than the initialTagSize of the tree.

matchingType - the matching type

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

fixedModifications - the fixed modifications to consider

variableModifications - the variable modifications to consider

limitXs - if true the share of Xs in the peptide sequences will be limited in order to increase sequencing speed.

reportFixedPtms - a boolean indicating whether fixed PTMs should be reported in the Peptide object

Returns:

the protein mapping for the given peptide sequence

Throws:

IOException

InterruptedException

ClassNotFoundException

SQLException

close

public void close()
           throws IOException,
                  SQLException

Closes all connections to files.

Throws:

IOException

SQLException

getCacheSize

public int getCacheSize()

Returns the size of the cache used for peptide mappings (note that there are two of them).

Returns:

the size of the cache used for peptide mappings

setCacheSize

public void setCacheSize(int cacheSize)

Sets the size of the cache used for peptide mappings (note that there are two of them).

Parameters:

cacheSize - the size of the cache used for peptide mappings

emptyCache

public void emptyCache()

Empties the cache.

reduceNodeCacheSize

public void reduceNodeCacheSize(double share)

Reduces the node cache size by the given share. If less than 100 nodes are left they will all be removed.

Parameters:

share - the share of the cache to remove. 0.5 means 50%

getNodesInCache

public int getNodesInCache()

Returns the number of nodes currently loaded in cache.

Returns:

the number of nodes currently loaded in cache

getMatchedPeptideSequences

public HashMap<String,ArrayList<Integer>> getMatchedPeptideSequences(String peptideSequence,
                                                            String proteinAccession,
                                                            AminoAcidPattern.MatchingType matchingType,
                                                            Double massTolerance,
                                                            boolean limitXs)
                                                              throws IOException,
                                                                     InterruptedException,
                                                                     ClassNotFoundException,
                                                                     SQLException

Returns a list of peptides matched using the given peptide sequence in the given protein according the provided matching settings.

Parameters:

peptideSequence - the original peptide sequence

proteinAccession - the accession of the protein of interest

matchingType - the matching type

massTolerance - the mass tolerance for indistinguishable amino acids matching mode

limitXs - if true the share of Xs in the peptide sequences will be limited in order to increase sequencing speed.

Returns:

a list of peptides matched and their indexes in the protein sequence

Throws:

IOException

InterruptedException

SQLException

ClassNotFoundException

getPeptideIterator

public ProteinTree.PeptideIterator getPeptideIterator()
                                               throws SQLException,
                                                      IOException,
                                                      ClassNotFoundException,
                                                      InterruptedException

Returns a PeptideIterator which iterates alphabetically all peptides corresponding to the end of a branch in the tree.

Returns:

a PeptideIterator which iterates alphabetically all peptides corresponding to the end of a branch in the tree

Throws:

SQLException

IOException

ClassNotFoundException

InterruptedException

getProteinLength

public Integer getProteinLength(String accession)
                         throws SQLException,
                                ClassNotFoundException,
                                IOException,
                                InterruptedException

Retrieves the length of a protein.

Parameters:

accession - the accession of the protein of interest

Returns:

the length of this protein

Throws:

SQLException

ClassNotFoundException

IOException

InterruptedException