public class SequenceFactory extends Object
Modifier and Type | Class and Description |
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class |
SequenceFactory.HeaderIterator
Convenience iterator iterating the headers of a FASTA file without using
the cache.
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class |
SequenceFactory.ProteinIterator
Convenience iterator iterating all proteins in a FASTA file without using
index or cache.
|
Modifier and Type | Field and Description |
---|---|
static long |
timeOut
The time out in milliseconds when querying the file.
|
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.
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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(int nThreads)
Returns the default protein tree corresponding to the database loaded in
factory.
|
ProteinTree |
getDefaultProteinTree(int nThreads,
WaitingHandler waitingHandler)
Returns the default protein tree corresponding to the database loaded in
factory.
|
ProteinTree |
getDefaultProteinTree(int nThreads,
WaitingHandler waitingHandler,
boolean displayProgress)
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.
|
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 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.
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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.
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static String |
reverseSequence(String sequence)
Reverses a protein sequence.
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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.
|
public static final long timeOut
public static SequenceFactory getInstance()
public static SequenceFactory getInstance(int nCache)
nCache
- the new cache sizepublic boolean hasEnoughSequences()
public void clearFactory() throws IOException, SQLException
IOException
SQLException
public void emptyCache()
public void reduceNodeCacheSize(double share)
share
- the share of the cache to remove. 0.5 means 50%public int getNodesInCache()
public Protein getProtein(String accession) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
accession
- accession of the desired proteinIOException
- thrown whenever an error is encountered while reading
the FASTA fileIllegalArgumentException
- thrown whenever an error is encountered
while reading the FASTA fileInterruptedException
FileNotFoundException
ClassNotFoundException
public Header getHeader(String accession) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
accession
- accession of the desired proteinIOException
- exception thrown whenever an error occurred while
reading the FASTA fileIllegalArgumentException
- exception thrown whenever a protein is
not foundInterruptedException
FileNotFoundException
ClassNotFoundException
public void loadFastaFile(File fastaFile) throws FileNotFoundException, IOException, ClassNotFoundException, StringIndexOutOfBoundsException, IllegalArgumentException
fastaFile
- the FASTA file to loadFileNotFoundException
- exception thrown if the file was not foundIOException
- exception thrown if an error occurred while reading
the FASTA fileClassNotFoundException
- exception thrown whenever an error
occurred while deserializing the file indexStringIndexOutOfBoundsException
- thrown if issues occur during the
parsing of the protein headersIllegalArgumentException
- if non unique accession numbers are
foundpublic void loadFastaFile(File fastaFile, WaitingHandler waitingHandler) throws FileNotFoundException, IOException, ClassNotFoundException, StringIndexOutOfBoundsException, IllegalArgumentException
fastaFile
- the FASTA file to loadwaitingHandler
- a waitingHandler showing the progressFileNotFoundException
- exception thrown if the file was not foundIOException
- exception thrown if an error occurred while reading
the FASTA fileClassNotFoundException
- exception thrown whenever an error
occurred while deserializing the file indexStringIndexOutOfBoundsException
- thrown if issues occur during the
parsing of the protein headersIllegalArgumentException
- if non unique accession numbers are
foundpublic boolean isClosed()
public void resetConnection() throws IOException
IOException
public static String getIndexName(String fastaName)
fastaName
- the name of the fasta filepublic void saveIndex() throws IOException
IOException
public void closeFile() throws IOException, SQLException
IOException
- exception thrown whenever an error occurred while
closing the fileSQLException
public static boolean isDecoy(String proteinAccession, String decoyFlag)
proteinAccession
- The accession of the proteindecoyFlag
- the decoy flagpublic boolean isDecoyAccession(String proteinAccession)
proteinAccession
- the protein accession of interest.public static boolean isDecoy(String proteinAccession)
proteinAccession
- the accession of interestpublic boolean concatenatedTargetDecoy()
public boolean isDefaultReversed()
public int getNTargetSequences()
public int getNSequences()
public void appendDecoySequences(File destinationFile) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
destinationFile
- the destination fileIOException
- exception thrown whenever an error occurred while
reading or writing a fileIllegalArgumentException
InterruptedException
FileNotFoundException
ClassNotFoundException
public void appendDecoySequences(File destinationFile, WaitingHandler waitingHandler) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
destinationFile
- the destination filewaitingHandler
- the waiting handlerIOException
- exception thrown whenever an error occurred while
reading or writing a fileIllegalArgumentException
- exception thrown whenever a protein is
not foundInterruptedException
FileNotFoundException
ClassNotFoundException
public static String reverseSequence(String sequence)
sequence
- the protein sequencepublic Set<String> getAccessions()
public int getnCache()
public void setnCache(int nCache)
nCache
- the new size of the cachepublic HashMap<String,Integer> getAAOccurrences(JProgressBar progressBar) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
progressBar
- a progress bar, can be nullIOException
- exception thrown whenever an error occurred while
reading the databaseIllegalArgumentException
InterruptedException
FileNotFoundException
ClassNotFoundException
public double computeMolecularWeight(String accession) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
accession
- the protein's accession numberIOException
IllegalArgumentException
InterruptedException
FileNotFoundException
ClassNotFoundException
public static String getTargetDecoyFileNameTag()
public static void setTargetDecoyFileNameTag(String targetDecoyFileNameTag)
targetDecoyFileNameTag
- the targetDecoyFileNameTag to setpublic String getFileName()
public File getCurrentFastaFile()
public static String getDefaultDecoyAccessionSuffix()
public static String getDefaultDecoyAccession(String targetAccession)
targetAccession
- the target accessionpublic static String getDefaultDecoyDescription(String targetDescription)
targetDescription
- the description of a target proteinpublic static String getDefaultTargetAccession(String decoyAccession)
decoyAccession
- the decoy accessionpublic FastaIndex getCurrentFastaIndex()
public ProteinTree getDefaultProteinTree() throws IOException, InterruptedException, ClassNotFoundException, IllegalArgumentException, SQLException
IOException
InterruptedException
ClassNotFoundException
IllegalArgumentException
SQLException
public ProteinTree getDefaultProteinTree(int nThreads) throws IOException, InterruptedException, ClassNotFoundException, IllegalArgumentException, SQLException
nThreads
- the number of threads to useIOException
InterruptedException
ClassNotFoundException
IllegalArgumentException
SQLException
public ProteinTree getDefaultProteinTree(WaitingHandler waitingHandler) throws IOException, InterruptedException, ClassNotFoundException, IllegalArgumentException, SQLException
waitingHandler
- waiting handler displaying progress to the user
during the initiation of the treeIOException
InterruptedException
ClassNotFoundException
IllegalArgumentException
SQLException
public ProteinTree getDefaultProteinTree(int nThreads, WaitingHandler waitingHandler) throws IOException, InterruptedException, ClassNotFoundException, IllegalArgumentException, SQLException
nThreads
- the number of threads to usewaitingHandler
- waiting handler displaying progress to the user
during the initiation of the treeIOException
InterruptedException
ClassNotFoundException
IllegalArgumentException
SQLException
public ProteinTree getDefaultProteinTree(int nThreads, WaitingHandler waitingHandler, boolean displayProgress) throws IOException, InterruptedException, ClassNotFoundException, IllegalArgumentException, SQLException
nThreads
- the number of threads to usewaitingHandler
- waiting handler displaying progress to the user
during the initiation of the treedisplayProgress
- display progressIOException
InterruptedException
ClassNotFoundException
IllegalArgumentException
SQLException
public boolean deleteProteinTree()
public SequenceFactory.HeaderIterator getHeaderIterator(boolean targetOnly) throws FileNotFoundException
targetOnly
- boolean indicating whether only target accessions shall
be iteratedFileNotFoundException
public SequenceFactory.ProteinIterator getProteinIterator(boolean targetOnly) throws FileNotFoundException
targetOnly
- boolean indicating whether only target accessions shall
be iteratedFileNotFoundException
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