SequenceFactory (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.experiment.identification.protein_sequences.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 int`	`minProteinCount` The minimal protein count required for reliable target/decoy based statistics.
`static long`	`TIME_OUT` The time out in milliseconds when querying the file.

Method Summary

All Methods Static Methods Instance Methods Concrete 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 in kDa.
`boolean`	`concatenatedTargetDecoy()` Indicates whether the database loaded contains decoy sequences.
`boolean`	`deleteProteinTree(ExceptionHandler exceptionHandler)` 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.
`Protein`	`getDecoyProteinFromTarget(String accession, boolean reindex)` Returns a decoy protein from a target protein or looks for the sequence in the cache if not found.
`Protein`	`getDecoyProteinFromTargetSynchronized(String accession, boolean reindex)` Returns a decoy protein from a target protein or looks for the sequence in the cache if not found.
`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.
`ProteinTree`	`getDefaultProteinTree(int nThreads, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler)` Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
`ProteinTree`	`getDefaultProteinTree(int nThreads, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, boolean displayProgress)` Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
`ProteinTree`	`getDefaultProteinTree(WaitingHandler waitingHandler, ExceptionHandler exceptionHandler)` Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
`static String`	`getDefaultTargetAccession(String decoyAccession)` Returns the default target accession of a given decoy protein.
`static FastaIndex`	`getFastaIndex(File fastaFile, boolean overwrite, WaitingHandler waitingHandler)` Returns the file index of the given FASTA file.
`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 String`	`getIndexName(String fastaName)` Returns the name of the FASTA index corresponding to the given FASTA file name.
`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.
`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, 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`	`isDecoyInMemory()` Returns whether decoys should be kept in memory.
`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)` Loads a new FASTA file in the factory.
`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`	`setDecoyInMemory(boolean decoyInMemory)` Sets whether decoys should be kept in memory.
`void`	`setnCache(int nCache)` Sets the size of the cache.
`static void`	`writeIndex(FastaIndex fastaIndex, File directory)` Serializes the FASTA file index in a given directory.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - TIME_OUT
```
public static final long TIME_OUT
```
    The time out in milliseconds when querying the file.
    
    See Also:
    
    Constant Field Values
  - minProteinCount
```
public static int minProteinCount
```
    The minimal protein count required for reliable target/decoy based statistics.
- 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 - if an IOException occurs
    
    SQLException - if an SQLException occurs
  - 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
```
    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 - if an InterruptedException occurs
    
    FileNotFoundException - if a FileNotFoundException occurs
  - getDecoyProteinFromTargetSynchronized
```
public Protein getDecoyProteinFromTargetSynchronized(String accession,
                                                     boolean reindex)
                                              throws IOException,
                                                     IllegalArgumentException,
                                                     FileNotFoundException
```
    Returns a decoy protein from a target protein or looks for the sequence in the cache if not found.
    
    Parameters:
    
    accession - the accession of the decoy protein to look for
    
    reindex - a boolean indicating whether the database should be re-indexed in case the protein is not found.
    
    Returns:
    
    the protein of interest, null if not found
    
    Throws:
    
    IOException - if an IOException occurs
    
    IllegalArgumentException - if an IllegalArgumentException occurs
    
    FileNotFoundException - if a FileNotFoundException occurs
  - getDecoyProteinFromTarget
```
public Protein getDecoyProteinFromTarget(String accession,
                                         boolean reindex)
                                  throws IOException,
                                         IllegalArgumentException,
                                         FileNotFoundException
```
    Returns a decoy protein from a target protein or looks for the sequence in the cache if not found.
    
    Parameters:
    
    accession - the accession of the decoy protein to look for
    
    reindex - a boolean indicating whether the database should be re-indexed in case the protein is not found.
    
    Returns:
    
    the protein of interest, null if not found
    
    Throws:
    
    IOException - if an IOException occurs
    
    IllegalArgumentException - if an IllegalArgumentException occurs
    
    FileNotFoundException - if a FileNotFoundException occurs
  - getHeader
```
public Header getHeader(String accession)
                 throws IOException,
                        InterruptedException
```
    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
    
    InterruptedException - exception thrown whenever an error occurred while waiting for the connection to the FASTA file to recover.
  - loadFastaFile
```
public void loadFastaFile(File fastaFile)
                   throws IOException,
                          ClassNotFoundException,
                          StringIndexOutOfBoundsException
```
    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:
    
    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
  - loadFastaFile
```
public void loadFastaFile(File fastaFile,
                          WaitingHandler waitingHandler)
                   throws IOException,
                          ClassNotFoundException,
                          StringIndexOutOfBoundsException
```
    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:
    
    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
  - 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 - if an IOException occurs
  - getFastaIndex
```
public static FastaIndex getFastaIndex(File fastaFile,
                                       boolean overwrite,
                                       WaitingHandler waitingHandler)
                                throws IOException,
                                       StringIndexOutOfBoundsException
```
    Returns the file index of the given FASTA file. If a problem occurs while reading an older index the file will be automatically overwritten and the stacktrace printed.
    
    Parameters:
    
    fastaFile - the FASTA file to index
    
    overwrite - boolean indicating whether the index .cui file shall be overwritten if present, even if the file has not been changed
    
    waitingHandler - a waitingHandler showing the progress
    
    Returns:
    
    the index of the FASTA file
    
    Throws:
    
    IOException - exception thrown if an error occurred while reading the FASTA file
    
    StringIndexOutOfBoundsException - thrown if issues occur during the parsing of the protein headers
    
    IllegalArgumentException - if non unique accession numbers are found
  - writeIndex
```
public static void writeIndex(FastaIndex fastaIndex,
                              File directory)
                       throws IOException
```
    Serializes the FASTA file index in a given directory.
    
    Parameters:
    
    fastaIndex - the index of the FASTA file
    
    directory - the directory where to write the file
    
    Throws:
    
    IOException - exception thrown whenever an error occurred while writing the file
  - getIndexName
```
public static String getIndexName(String fastaName)
```
    Returns the name of the FASTA index corresponding to the given FASTA file name.
    
    Parameters:
    
    fastaName - the name of the FASTA file
    
    Returns:
    
    the name of the index
  - saveIndex
```
public void saveIndex()
               throws IOException
```
    Saves the index.
    
    Throws:
    
    IOException - if an IOException occurs
  - closeFile
```
public void closeFile()
               throws IOException,
                      SQLException
```
    Closes the opened file.
    
    Throws:
    
    IOException - exception thrown whenever an error occurred while closing the file
    
    SQLException - if an SQLException occurs
  - 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
  - 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,
                                 InterruptedException,
                                 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
    
    InterruptedException - if an InterruptedException occurs
    
    ClassNotFoundException - if an ClassNotFoundException occurs
  - appendDecoySequences
```
public void appendDecoySequences(File destinationFile,
                                 WaitingHandler waitingHandler)
                          throws IOException,
                                 InterruptedException,
                                 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
    
    InterruptedException - if an InterruptedException occurs
    
    ClassNotFoundException - if an ClassNotFoundException occurs
  - 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,
                                                InterruptedException,
                                                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
    
    InterruptedException - if an InterruptedException occurs
    
    ClassNotFoundException - if an ClassNotFoundException occurs
  - computeMolecularWeight
```
public double computeMolecularWeight(String accession)
                              throws IOException,
                                     InterruptedException,
                                     ClassNotFoundException
```
    Returns the protein's molecular weight in kDa.
    
    Parameters:
    
    accession - the protein's accession number
    
    Returns:
    
    the protein's molecular weight
    
    Throws:
    
    IOException - exception thrown whenever an error occurred while reading the protein sequence
    
    InterruptedException - exception thrown whenever an error occurred while reading the protein sequence
    
    ClassNotFoundException - exception thrown whenever an error occurred while reading the protein sequence
  - 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()
```
    Returns the default protein tree. Null if none created.
    
    Returns:
    
    the default protein tree
  - getDefaultProteinTree
```
public ProteinTree getDefaultProteinTree(WaitingHandler waitingHandler,
                                         ExceptionHandler exceptionHandler)
                                  throws IOException,
                                         InterruptedException,
                                         ClassNotFoundException,
                                         SQLException
```
    Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
    
    Parameters:
    
    waitingHandler - waiting handler displaying progress to the user during the initiation of the tree
    
    exceptionHandler - handler for the exceptions encountered while creating the tree
    
    Returns:
    
    the default protein tree
    
    Throws:
    
    IOException - exception thrown whenever an error occurs while reading or writing a file.
    
    ClassNotFoundException - exception thrown whenever an error occurs while deserializing an object.
    
    InterruptedException - exception thrown whenever a threading issue occurred while interacting with the tree.
    
    SQLException - if an SQLException exception thrown whenever a problem occurred while interacting with the tree database.
  - getDefaultProteinTree
```
public ProteinTree getDefaultProteinTree(int nThreads,
                                         WaitingHandler waitingHandler,
                                         ExceptionHandler exceptionHandler)
                                  throws IOException,
                                         InterruptedException,
                                         ClassNotFoundException,
                                         SQLException
```
    Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
    
    Parameters:
    
    nThreads - the number of threads to use
    
    waitingHandler - waiting handler displaying progress to the user during the initiation of the tree
    
    exceptionHandler - handler for the exceptions encountered while creating the tree
    
    Returns:
    
    the default protein tree
    
    Throws:
    
    IOException - exception thrown whenever an error occurs while reading or writing a file.
    
    ClassNotFoundException - exception thrown whenever an error occurs while deserializing an object.
    
    InterruptedException - exception thrown whenever a threading issue occurred while interacting with the tree.
    
    SQLException - if an SQLException exception thrown whenever a problem occurred while interacting with the tree database.
  - getDefaultProteinTree
```
public ProteinTree getDefaultProteinTree(int nThreads,
                                         WaitingHandler waitingHandler,
                                         ExceptionHandler exceptionHandler,
                                         boolean displayProgress)
                                  throws IOException,
                                         InterruptedException,
                                         ClassNotFoundException,
                                         SQLException
```
    Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
    
    Parameters:
    
    nThreads - the number of threads to use
    
    waitingHandler - waiting handler displaying progress to the user during the initiation of the tree
    
    exceptionHandler - handler for the exceptions encountered while creating the tree
    
    displayProgress - display progress
    
    Returns:
    
    the default protein tree
    
    Throws:
    
    IOException - exception thrown whenever an error occurs while reading or writing a file.
    
    ClassNotFoundException - exception thrown whenever an error occurs while deserializing an object.
    
    InterruptedException - exception thrown whenever a threading issue occurred while interacting with the tree.
    
    SQLException - if an SQLException exception thrown whenever a problem occurred while interacting with the tree database.
  - deleteProteinTree
```
public boolean deleteProteinTree(ExceptionHandler exceptionHandler)
```
    Try to delete the default protein tree.
    
    Parameters:
    
    exceptionHandler - handler for the exceptions encountered while creating the 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 - if a FileNotFoundException occurs
  - 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 - if a FileNotFoundException occurs
  - isDecoyInMemory
```
public boolean isDecoyInMemory()
```
    Returns whether decoys should be kept in memory.
    
    Returns:
    
    true if decoys should be kept in memory
  - setDecoyInMemory
```
public void setDecoyInMemory(boolean decoyInMemory)
```
    Sets whether decoys should be kept in memory.
    
    Parameters:
    
    decoyInMemory - true if decoys should be kept in memory

Class SequenceFactory

Nested Class Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

TIME_OUT

minProteinCount

Method Detail

getInstance

getInstance

hasEnoughSequences

clearFactory

emptyCache

reduceNodeCacheSize

getNodesInCache

getProtein

getDecoyProteinFromTargetSynchronized

getDecoyProteinFromTarget

getHeader

loadFastaFile

loadFastaFile

isClosed

resetConnection

getFastaIndex

writeIndex

getIndexName

saveIndex

closeFile

isDecoy

isDecoyAccession

concatenatedTargetDecoy

isDefaultReversed

getNTargetSequences

getNSequences

appendDecoySequences

appendDecoySequences

reverseSequence

getAccessions

getnCache

setnCache

getAAOccurrences

computeMolecularWeight

getFileName

getCurrentFastaFile

getDefaultDecoyAccessionSuffix

getDefaultDecoyAccession

getDefaultDecoyDescription

getDefaultTargetAccession

getCurrentFastaIndex

getDefaultProteinTree

getDefaultProteinTree

getDefaultProteinTree

getDefaultProteinTree

deleteProteinTree

getHeaderIterator

getProteinIterator

isDecoyInMemory

setDecoyInMemory