com.compomics.util.experiment.identification

Class SequenceFactory

java.lang.Object

com.compomics.util.experiment.identification.SequenceFactory

public class SequenceFactory
extends Object

Factory retrieving the information of the loaded FASTA file.

Author:

Marc Vaudel, Harald Barsnes

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	SequenceFactory.HeaderIterator Convenience iterator iterating the headers of a FASTA file without using the cache.
class	SequenceFactory.ProteinIterator Convenience iterator iterating all proteins in a FASTA file without using index or cache.

Field Summary

Fields

Modifier and Type	Field and Description
static long	timeOut The time out in milliseconds when querying the file.

Method Summary

Methods

Modifier and Type	Method and Description
void	appendDecoySequences(File destinationFile) Appends decoy sequences to the desired file.
void	appendDecoySequences(File destinationFile, WaitingHandler waitingHandler) Appends decoy sequences to the desired file while displaying progress.
void	clearFactory() Clears the factory getInstance() needs to be called afterwards.
void	closeFile() Closes the opened file.
double	computeMolecularWeight(String accession) Returns the protein's molecular weight.
boolean	concatenatedTargetDecoy() Indicates whether the database loaded contains decoy sequences.
boolean	deleteProteinTree() Try to delete the default protein tree.
void	emptyCache() Empties the cache of the factory.
HashMap<String,Integer>	getAAOccurrences(JProgressBar progressBar) Returns the occurrence of every amino acid in the database.
Set<String>	getAccessions() Returns the sequences present in the database.
File	getCurrentFastaFile() Returns the currently loaded fasta file.
FastaIndex	getCurrentFastaIndex() Returns the FASTA index of the currently loaded file.
static String	getDefaultDecoyAccession(String targetAccession) Returns the default decoy accession for a target accession.
static String	getDefaultDecoyAccessionSuffix() Returns the default suffix for a decoy accession.
static String	getDefaultDecoyDescription(String targetDescription) Returns the default description for a decoy protein.
ProteinTree	getDefaultProteinTree() Returns the default protein tree corresponding to the database loaded in factory.
ProteinTree	getDefaultProteinTree(WaitingHandler waitingHandler) Returns the default protein tree corresponding to the database loaded in factory.
ProteinTree	getDefaultProteinTree(WaitingHandler waitingHandler, boolean displayProgress) Returns the default protein tree corresponding to the database loaded in factory
static String	getDefaultTargetAccession(String decoyAccession) Returns the default target accession of a given decoy protein.
String	getFileName() Returns the name of the loaded FASTA file.
Header	getHeader(String accession) Returns the desired header for the protein in the FASTA file.
SequenceFactory.HeaderIterator	getHeaderIterator(boolean targetOnly) Returns an iterator of all the headers in the FASTA file.
static SequenceFactory	getInstance() Static method returning the instance of the factory.
static SequenceFactory	getInstance(int nCache) Returns the instance of the factory with the specified cache size.
int	getnCache() Returns the size of the cache.
int	getNodesInCache() Returns the number of nodes currently loaded in cache.
int	getNSequences() Returns the number of sequences in the FASTA file.
int	getNTargetSequences() Returns the number of target sequences in the database.
Protein	getProtein(String accession) Returns the desired protein.
SequenceFactory.ProteinIterator	getProteinIterator(boolean targetOnly) Returns an iterator of all the proteins in the FASTA file.
static String	getTargetDecoyFileNameTag() Returns the target-decoy file name tag.
boolean	hasEnoughSequences() Indicates whether the database contained enough protein sequences for reliability of the target/decoy based statistics.
boolean	isClosed() Indicates whether the connection to the random access file has been closed.
static boolean	isDecoy(String proteinAccession) Deprecated. deprecated, use the isDecoy(proteinAccession, flag) with file dependent flag or isDecoyAccession(String proteinAccession) instead.
static boolean	isDecoy(String proteinAccession, String decoyFlag) Returns a boolean indicating whether a protein is decoy or not based on the protein accession and a given decoy flag.
boolean	isDecoyAccession(String proteinAccession) Indicates whether a protein is a decoy in the selected loaded FASTA file.
boolean	isDefaultReversed() Indicates whether the decoy sequences are reversed versions of the target and the decoy accessions built based on the sequence factory methods.
void	loadFastaFile(File fastaFile) Deprecated. use the version with the WaitingHandler instead
void	loadFastaFile(File fastaFile, WaitingHandler waitingHandler) Loads a new FASTA file in the factory.
void	reduceNodeCacheSize(double share) Reduces the node cache size of the protein tree by the given share.
void	resetConnection() Resets the connection to the random access file.
static String	reverseSequence(String sequence) Reverses a protein sequence.
void	saveIndex() Saves the index.
void	setnCache(int nCache) Sets the size of the cache.
static void	setTargetDecoyFileNameTag(String targetDecoyFileNameTag) Set the target-decoy file name tag.

Methods inherited from class java.lang.Object

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

Field Detail

timeOut

public static final long timeOut

The time out in milliseconds when querying the file.

See Also:

Constant Field Values

Method Detail

getInstance

public static SequenceFactory getInstance()

Static method returning the instance of the factory.

Returns:

the instance of the factory

getInstance

public static SequenceFactory getInstance(int nCache)

Returns the instance of the factory with the specified cache size.

Parameters:

nCache - the new cache size

Returns:

the instance of the factory with the specified cache size

hasEnoughSequences

public boolean hasEnoughSequences()

Indicates whether the database contained enough protein sequences for reliability of the target/decoy based statistics.

Returns:

a boolean indicating whether the database contained enough protein sequences for reliability of the target/decoy based statistics

clearFactory

public void clearFactory()
                  throws IOException,
                         SQLException

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

Throws:

IOException

SQLException

emptyCache

public void emptyCache()

Empties the cache of the factory.

reduceNodeCacheSize

public void reduceNodeCacheSize(double share)

Reduces the node cache size of the protein tree by the given share.

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

getProtein

public Protein getProtein(String accession)
                   throws IOException,
                          IllegalArgumentException,
                          InterruptedException,
                          FileNotFoundException,
                          ClassNotFoundException

Returns the desired protein. If the protein is not found, the database will be re-indexed.

Parameters:

accession - accession of the desired protein

Returns:

the desired protein

Throws:

IOException - thrown whenever an error is encountered while reading the FASTA file

IllegalArgumentException - thrown whenever an error is encountered while reading the FASTA file

InterruptedException

FileNotFoundException

ClassNotFoundException

getHeader

public Header getHeader(String accession)
                 throws IOException,
                        IllegalArgumentException,
                        InterruptedException,
                        FileNotFoundException,
                        ClassNotFoundException

Returns the desired header for the protein in the FASTA file.

Parameters:

accession - accession of the desired protein

Returns:

the corresponding header

Throws:

IOException - exception thrown whenever an error occurred while reading the FASTA file

IllegalArgumentException - exception thrown whenever a protein is not found

InterruptedException

FileNotFoundException

ClassNotFoundException

loadFastaFile

public void loadFastaFile(File fastaFile)
                   throws FileNotFoundException,
                          IOException,
                          ClassNotFoundException,
                          StringIndexOutOfBoundsException,
                          IllegalArgumentException

Deprecated. use the version with the WaitingHandler instead

Loads a new FASTA file in the factory. Only one FASTA file can be loaded at a time.

Parameters:

fastaFile - the FASTA file to load

Throws:

FileNotFoundException - exception thrown if the file was not found

IOException - exception thrown if an error occurred while reading the FASTA file

ClassNotFoundException - exception thrown whenever an error occurred while deserializing the file index

StringIndexOutOfBoundsException - thrown if issues occur during the parsing of the protein headers

IllegalArgumentException - if non unique accession numbers are found

loadFastaFile

public void loadFastaFile(File fastaFile,
                 WaitingHandler waitingHandler)
                   throws FileNotFoundException,
                          IOException,
                          ClassNotFoundException,
                          StringIndexOutOfBoundsException,
                          IllegalArgumentException

Loads a new FASTA file in the factory. Only one FASTA file can be loaded at a time.

Parameters:

fastaFile - the FASTA file to load

waitingHandler - a waitingHandler showing the progress

Throws:

FileNotFoundException - exception thrown if the file was not found

IOException - exception thrown if an error occurred while reading the FASTA file

ClassNotFoundException - exception thrown whenever an error occurred while deserializing the file index

StringIndexOutOfBoundsException - thrown if issues occur during the parsing of the protein headers

IllegalArgumentException - if non unique accession numbers are found

isClosed

public boolean isClosed()

Indicates whether the connection to the random access file has been closed.

Returns:

a boolean indicating whether the connection to the random access file has been closed.

resetConnection

public void resetConnection()
                     throws IOException

Resets the connection to the random access file.

Throws:

IOException

saveIndex

public void saveIndex()
               throws IOException

Saves the index.

Throws:

IOException

closeFile

public void closeFile()
               throws IOException,
                      SQLException

Closes the opened file.

Throws:

IOException - exception thrown whenever an error occurred while closing the file

SQLException

isDecoy

public static boolean isDecoy(String proteinAccession,
              String decoyFlag)

Returns a boolean indicating whether a protein is decoy or not based on the protein accession and a given decoy flag. Note: in most cases the faster isDecoyAccession method should be used instead!

Parameters:

proteinAccession - The accession of the protein

decoyFlag - the decoy flag

Returns:

a boolean indicating whether the protein is Decoy.

isDecoyAccession

public boolean isDecoyAccession(String proteinAccession)

Indicates whether a protein is a decoy in the selected loaded FASTA file.

Parameters:

proteinAccession - the protein accession of interest.

Returns:

true if decoy

isDecoy

public static boolean isDecoy(String proteinAccession)

Deprecated. deprecated, use the isDecoy(proteinAccession, flag) with file dependent flag or isDecoyAccession(String proteinAccession) instead.

Indicates whether a protein accession is decoy according to the standard decoy flags.

Parameters:

proteinAccession - the accession of interest

Returns:

true if decoy

concatenatedTargetDecoy

public boolean concatenatedTargetDecoy()

Indicates whether the database loaded contains decoy sequences.

Returns:

a boolean indicating whether the database loaded contains decoy sequences

isDefaultReversed

public boolean isDefaultReversed()

Indicates whether the decoy sequences are reversed versions of the target and the decoy accessions built based on the sequence factory methods. See getDefaultDecoyAccession(String targetAccession).

Returns:

true if the the decoy sequences are reversed versions of the target and the decoy accessions built based on the sequence factory method

getNTargetSequences

public int getNTargetSequences()

Returns the number of target sequences in the database.

Returns:

the number of target sequences in the database

getNSequences

public int getNSequences()

Returns the number of sequences in the FASTA file.

Returns:

the number of sequences in the FASTA file

appendDecoySequences

public void appendDecoySequences(File destinationFile)
                          throws IOException,
                                 IllegalArgumentException,
                                 InterruptedException,
                                 FileNotFoundException,
                                 ClassNotFoundException

Appends decoy sequences to the desired file.

Parameters:

destinationFile - the destination file

Throws:

IOException - exception thrown whenever an error occurred while reading or writing a file

IllegalArgumentException

InterruptedException

FileNotFoundException

ClassNotFoundException

appendDecoySequences

public void appendDecoySequences(File destinationFile,
                        WaitingHandler waitingHandler)
                          throws IOException,
                                 IllegalArgumentException,
                                 InterruptedException,
                                 FileNotFoundException,
                                 ClassNotFoundException

Appends decoy sequences to the desired file while displaying progress.

Parameters:

destinationFile - the destination file

waitingHandler - the waiting handler

Throws:

IOException - exception thrown whenever an error occurred while reading or writing a file

IllegalArgumentException - exception thrown whenever a protein is not found

InterruptedException

FileNotFoundException

ClassNotFoundException

reverseSequence

public static String reverseSequence(String sequence)

Reverses a protein sequence.

Parameters:

sequence - the protein sequence

Returns:

the reversed protein sequence

getAccessions

public Set<String> getAccessions()

Returns the sequences present in the database. An empty list if no file is loaded.

Returns:

the sequences present in the database

getnCache

public int getnCache()

Returns the size of the cache.

Returns:

the size of the cache

setnCache

public void setnCache(int nCache)

Sets the size of the cache.

Parameters:

nCache - the new size of the cache

getAAOccurrences

public HashMap<String,Integer> getAAOccurrences(JProgressBar progressBar)
                                         throws IOException,
                                                IllegalArgumentException,
                                                InterruptedException,
                                                FileNotFoundException,
                                                ClassNotFoundException

Returns the occurrence of every amino acid in the database.

Parameters:

progressBar - a progress bar, can be null

Returns:

a map containing all amino acid occurrence in the database

Throws:

IOException - exception thrown whenever an error occurred while reading the database

IllegalArgumentException

InterruptedException

FileNotFoundException

ClassNotFoundException

computeMolecularWeight

public double computeMolecularWeight(String accession)
                              throws IOException,
                                     IllegalArgumentException,
                                     InterruptedException,
                                     FileNotFoundException,
                                     ClassNotFoundException

Returns the protein's molecular weight.

Parameters:

accession - the protein's accession number

Returns:

the protein's molecular weight

Throws:

IOException

IllegalArgumentException

InterruptedException

FileNotFoundException

ClassNotFoundException

getTargetDecoyFileNameTag

public static String getTargetDecoyFileNameTag()

Returns the target-decoy file name tag.

Returns:

the targetDecoyFileNameTag

setTargetDecoyFileNameTag

public static void setTargetDecoyFileNameTag(String targetDecoyFileNameTag)

Set the target-decoy file name tag.

Parameters:

targetDecoyFileNameTag - the targetDecoyFileNameTag to set

getFileName

public String getFileName()

Returns the name of the loaded FASTA file. Null if none loaded.

Returns:

the name of the loaded FASTA file

getCurrentFastaFile

public File getCurrentFastaFile()

Returns the currently loaded fasta file.

Returns:

the currently loaded fasta file

getDefaultDecoyAccessionSuffix

public static String getDefaultDecoyAccessionSuffix()

Returns the default suffix for a decoy accession.

Returns:

the default suffix for a decoy accession

getDefaultDecoyAccession

public static String getDefaultDecoyAccession(String targetAccession)

Returns the default decoy accession for a target accession.

Parameters:

targetAccession - the target accession

Returns:

the default decoy accession

getDefaultDecoyDescription

public static String getDefaultDecoyDescription(String targetDescription)

Returns the default description for a decoy protein.

Parameters:

targetDescription - the description of a target protein

Returns:

the default description of the decoy protein

getDefaultTargetAccession

public static String getDefaultTargetAccession(String decoyAccession)

Returns the default target accession of a given decoy protein. Note: works only for the accessions constructed according to getDefaultDecoyAccession(String targetAccession).

Parameters:

decoyAccession - the decoy accession

Returns:

the target accession

getCurrentFastaIndex

public FastaIndex getCurrentFastaIndex()

Returns the FASTA index of the currently loaded file.

Returns:

the FASTA index of the currently loaded file

getDefaultProteinTree

public ProteinTree getDefaultProteinTree()
                                  throws IOException,
                                         InterruptedException,
                                         ClassNotFoundException,
                                         IllegalArgumentException,
                                         SQLException

Returns the default protein tree corresponding to the database loaded in factory.

Returns:

the default protein tree

Throws:

IOException

InterruptedException

ClassNotFoundException

IllegalArgumentException

SQLException

getDefaultProteinTree

public ProteinTree getDefaultProteinTree(WaitingHandler waitingHandler)
                                  throws IOException,
                                         InterruptedException,
                                         ClassNotFoundException,
                                         IllegalArgumentException,
                                         SQLException

Returns the default protein tree corresponding to the database loaded in factory.

Parameters:

waitingHandler - waiting handler displaying progress to the user during the initiation of the tree

Returns:

the default protein tree

Throws:

IOException

InterruptedException

ClassNotFoundException

IllegalArgumentException

SQLException

getDefaultProteinTree

public ProteinTree getDefaultProteinTree(WaitingHandler waitingHandler,
                                boolean displayProgress)
                                  throws IOException,
                                         InterruptedException,
                                         ClassNotFoundException,
                                         IllegalArgumentException,
                                         SQLException

Returns the default protein tree corresponding to the database loaded in factory

Parameters:

waitingHandler - waiting handler displaying progress to the user during the initiation of the tree

displayProgress - display progress

Returns:

the default protein tree

Throws:

IOException

InterruptedException

ClassNotFoundException

IllegalArgumentException

SQLException

deleteProteinTree

public boolean deleteProteinTree()

Try to delete the default protein tree.

Returns:

true of the deletion was a success

getHeaderIterator

public SequenceFactory.HeaderIterator getHeaderIterator(boolean targetOnly)
                                                 throws FileNotFoundException

Returns an iterator of all the headers in the FASTA file. Note: when reaching the end of the file the connection will be closed. Do it using the close() method if the end is never reached.

Parameters:

targetOnly - boolean indicating whether only target accessions shall be iterated

Returns:

a header iterator.

Throws:

FileNotFoundException

getProteinIterator

public SequenceFactory.ProteinIterator getProteinIterator(boolean targetOnly)
                                                   throws FileNotFoundException

Returns an iterator of all the proteins in the FASTA file. Note: when reaching the end of the file the connection will be closed. Do it using the close() method if the end is never reached.

Parameters:

targetOnly - boolean indicating whether only target accessions shall be iterated

Returns:

a protein iterator.

Throws:

FileNotFoundException