public class SequenceFactory extends Object
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.
|
void |
emptyCache()
Empties the cache of the factory.
|
HashMap<String,Integer> |
getAAOccurrences(JProgressBar progressBar)
Returns the occurrence of every amino acid in the database.
|
ArrayList<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 |
getDecoyFlag(String proteinAccession)
Returns the default tag matched in the sequence if any.
|
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.
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static String |
getDefaultDecoyDescription(String targetDescription)
Returns the default description for a decoy protein.
|
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.
|
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 |
getNTargetSequences()
Returns the number of target sequences in the database.
|
Protein |
getProtein(String accession)
Returns the desired protein.
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static String |
getTargetDecoyFileNameTag()
Returns the target-decoy file name tag.
|
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 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)
Loads a new FASTA file in the factory.
|
void |
loadFastaFile(File fastaFile,
WaitingHandler waitingHandler)
Loads a new FASTA file in the factory.
|
static String |
reverseSequence(String sequence)
Reverses a protein sequence.
|
void |
saveIndex()
Saves the index.
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void |
setnCache(int nCache)
Sets the size of the cache.
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static void |
setTargetDecoyFileNameTag(String targetDecoyFileNameTag)
Set the target-decoy file name tag.
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public static SequenceFactory getInstance()
public static SequenceFactory getInstance(int nCache)
nCache
- the new cache sizepublic void clearFactory() throws IOException
IOException
public void emptyCache()
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 void saveIndex() throws IOException
IOException
public void closeFile() throws IOException
IOException
- exception thrown whenever an error occurred while
closing the filepublic static boolean isDecoy(String proteinAccession, String decoyFlag)
proteinAccession
- The accession of the proteindecoyFlag
- the decoy flagpublic static String getDecoyFlag(String proteinAccession)
proteinAccession
- the protein accessionpublic 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 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 ArrayList<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()
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