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java.lang.Objectcom.compomics.util.experiment.identification.SequenceFactory
public class SequenceFactory
factory retrieving the information of the loaded fasta file
Field Summary | |
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static String[] |
decoyFlags
Recognized flags for a decoy protein |
Method Summary | |
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void |
appendDecoySequences(File destinationFile)
Appends decoy sequences to the desired file |
void |
appendDecoySequences(File destinationFile,
ProgressDialogX progressDialog)
Appends decoy sequences to the desired file while displaying progress |
void |
closeFile()
Closes the opened file |
boolean |
concatenatedTargetDecoy()
Indicates whether the database loaded contains decoy sequences |
static FastaIndex |
createFastaIndex(File fastaFile)
static method to create a fasta index for a fasta file |
static FastaIndex |
createFastaIndex(File fastaFile,
ProgressDialogX progressDialog)
static method to create a fasta index for a fasta file |
ArrayList<String> |
getAccessions()
Returns the sequences present in the database |
FastaIndex |
getFastaIndex(File fastaFile)
Returns the file index of a fasta file |
FastaIndex |
getFastaIndex(File fastaFile,
ProgressDialogX progressDialog)
Returns the file index of a fasta file |
Header |
getHeader(String accession)
returns the desired header for the protein in the fasta file |
FastaIndex |
getIndex(File fastaIndex)
Deserializes the index of 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 |
static boolean |
isDecoy(String proteinAccession)
Returns a boolean indicating whether a protein is decoy or not based on the protein accession. |
void |
loadFastaFile(File fastaFile)
loads a new fasta file in the factory. |
void |
loadFastaFile(File fastaFile,
ProgressDialogX progressDialog)
loads a new fasta file in the factory. |
void |
setnCache(int nCache)
Sets the size of the cache |
void |
writeIndex(FastaIndex fastaIndex,
File directory)
serializes the fasta file index in a given directory |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String[] decoyFlags
Method Detail |
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public static SequenceFactory getInstance()
public static SequenceFactory getInstance(int nCache)
nCache
- the new cache size
public Protein getProtein(String accession) throws IOException
accession
- accession of the desired protein
IOException
- exception thrown whenever an error is encountered while reading the fasta filepublic Header getHeader(String accession) throws IOException
accession
- accession of the desired protein
IOException
- exception thrown whenever an error occurred while reading the fasta filepublic void loadFastaFile(File fastaFile) throws FileNotFoundException, IOException, ClassNotFoundException
fastaFile
- the fasta file to load
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 indexpublic void loadFastaFile(File fastaFile, ProgressDialogX progressDialog) throws FileNotFoundException, IOException, ClassNotFoundException
fastaFile
- the fasta file to loadprogressDialog
- a progress dialog showing the progress
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 indexpublic FastaIndex getFastaIndex(File fastaFile) throws FileNotFoundException, IOException, ClassNotFoundException
fastaFile
- the fasta file
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 indexpublic FastaIndex getFastaIndex(File fastaFile, ProgressDialogX progressDialog) throws FileNotFoundException, IOException, ClassNotFoundException
fastaFile
- the fasta fileprogressDialog
- a progress dialog showing the progress
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 indexpublic void writeIndex(FastaIndex fastaIndex, File directory) throws IOException
fastaIndex
- the index of the fasta filedirectory
- the directory where to write the file
IOException
- exception thrown whenever an error occurred while writing the filepublic FastaIndex getIndex(File fastaIndex) throws FileNotFoundException, IOException, ClassNotFoundException
fastaIndex
- the fasta cui index file
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 indexpublic void closeFile() throws IOException
IOException
- exception thrown whenever an error occurred while closing the filepublic static FastaIndex createFastaIndex(File fastaFile) throws FileNotFoundException, IOException
fastaFile
- the fasta file
FileNotFoundException
- exception thrown if the fasta file was not found
IOException
- exception thrown whenever an error occurred while reading the filepublic static FastaIndex createFastaIndex(File fastaFile, ProgressDialogX progressDialog) throws FileNotFoundException, IOException
fastaFile
- the fasta fileprogressDialog
- a progress dialog showing the progress
FileNotFoundException
- exception thrown if the fasta file was not found
IOException
- exception thrown whenever an error occurred while reading the filepublic static boolean isDecoy(String proteinAccession)
proteinAccession
- The accession of the protein
public boolean concatenatedTargetDecoy()
public int getNTargetSequences()
public void appendDecoySequences(File destinationFile) throws IOException
destinationFile
- the destination file
IOException
- exception thrown whenever an error occurred while reading or writing a filepublic void appendDecoySequences(File destinationFile, ProgressDialogX progressDialog) throws IOException
destinationFile
- the destination fileprogressDialog
- the progress dialog
IOException
- exception thrown whenever an error occurred while reading or writing a filepublic ArrayList<String> getAccessions()
public int getnCache()
public void setnCache(int nCache)
nCache
- the new size of the cache
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