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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 java.lang.String[] |
decoyFlags
Recognized flags for a decoy protein |
Method Summary | |
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void |
appendDecoySequences(java.io.File destinationFile)
Appends decoy sequences to the desired file. |
void |
appendDecoySequences(java.io.File destinationFile,
javax.swing.JProgressBar progressBar)
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(java.io.File fastaFile)
Static method to create a FASTA index for a FASTA file. |
static FastaIndex |
createFastaIndex(java.io.File fastaFile,
javax.swing.JProgressBar progressBar)
Static method to create a FASTA index for a FASTA file. |
java.util.HashMap<java.lang.String,java.lang.Integer> |
getAAOccurrences(javax.swing.JProgressBar progressBar)
Returns the occurrence of every amino acid in the database |
java.util.ArrayList<java.lang.String> |
getAccessions()
Returns the sequences present in the database. |
FastaIndex |
getFastaIndex(java.io.File fastaFile)
Returns the file index of a FASTA file. |
FastaIndex |
getFastaIndex(java.io.File fastaFile,
javax.swing.JProgressBar progressBar)
Returns the file index of a FASTA file. |
Header |
getHeader(java.lang.String accession)
Returns the desired header for the protein in the FASTA file. |
FastaIndex |
getIndex(java.io.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(java.lang.String accession)
Returns the desired protein. |
static boolean |
isDecoy(java.lang.String proteinAccession)
Returns a boolean indicating whether a protein is decoy or not based on the protein accession. |
void |
loadFastaFile(java.io.File fastaFile)
Loads a new FASTA file in the factory. |
void |
loadFastaFile(java.io.File fastaFile,
javax.swing.JProgressBar progressBar)
Loads a new FASTA file in the factory. |
void |
setnCache(int nCache)
Sets the size of the cache. |
void |
writeIndex(FastaIndex fastaIndex,
java.io.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 java.lang.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(java.lang.String accession) throws java.io.IOException, java.lang.IllegalArgumentException
accession
- accession of the desired protein
java.io.IOException
- thrown whenever an error is encountered while reading
the FASTA file
java.lang.IllegalArgumentException
- thrown whenever an error is encountered
while reading the FASTA filepublic Header getHeader(java.lang.String accession) throws java.io.IOException, java.lang.IllegalArgumentException
accession
- accession of the desired protein
java.io.IOException
- exception thrown whenever an error occurred while
reading the FASTA file
java.lang.IllegalArgumentException
- exception thrown whenever a protein is
not foundpublic void loadFastaFile(java.io.File fastaFile) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException
fastaFile
- the FASTA file to load
java.io.FileNotFoundException
- exception thrown if the file was not found
java.io.IOException
- exception thrown if an error occurred while reading
the FASTA file
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while deserializing the file indexpublic void loadFastaFile(java.io.File fastaFile, javax.swing.JProgressBar progressBar) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException
fastaFile
- the FASTA file to loadprogressBar
- a progress bar showing the progress
java.io.FileNotFoundException
- exception thrown if the file was not found
java.io.IOException
- exception thrown if an error occurred while reading
the FASTA file
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while deserializing the file indexpublic FastaIndex getFastaIndex(java.io.File fastaFile) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException
fastaFile
- the FASTA file
java.io.FileNotFoundException
- exception thrown if the file was not found
java.io.IOException
- exception thrown if an error occurred while reading
the FASTA file
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while deserializing the file indexpublic FastaIndex getFastaIndex(java.io.File fastaFile, javax.swing.JProgressBar progressBar) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException
fastaFile
- the FASTA fileprogressBar
- a progress bar showing the progress
java.io.FileNotFoundException
- exception thrown if the file was not found
java.io.IOException
- exception thrown if an error occurred while reading
the FASTA file
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while deserializing the file indexpublic void writeIndex(FastaIndex fastaIndex, java.io.File directory) throws java.io.IOException
fastaIndex
- the index of the FASTA filedirectory
- the directory where to write the file
java.io.IOException
- exception thrown whenever an error occurred while
writing the filepublic FastaIndex getIndex(java.io.File fastaIndex) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException
fastaIndex
- the FASTA cui index file
java.io.FileNotFoundException
- exception thrown if the file was not found
java.io.IOException
- exception thrown if an error occurred while reading
the FASTA file
java.lang.ClassNotFoundException
- exception thrown whenever an error
occurred while deserializing the file indexpublic void closeFile() throws java.io.IOException
java.io.IOException
- exception thrown whenever an error occurred while
closing the filepublic static FastaIndex createFastaIndex(java.io.File fastaFile) throws java.io.FileNotFoundException, java.io.IOException
fastaFile
- the FASTA file
java.io.FileNotFoundException
- exception thrown if the FASTA file was not
found
java.io.IOException
- exception thrown whenever an error occurred while
reading the filepublic static FastaIndex createFastaIndex(java.io.File fastaFile, javax.swing.JProgressBar progressBar) throws java.io.FileNotFoundException, java.io.IOException
fastaFile
- the FASTA fileprogressBar
- a progress bar showing the progress
java.io.FileNotFoundException
- exception thrown if the FASTA file was not
found
java.io.IOException
- exception thrown whenever an error occurred while
reading the filepublic static boolean isDecoy(java.lang.String proteinAccession)
proteinAccession
- The accession of the protein
public boolean concatenatedTargetDecoy()
public int getNTargetSequences()
public void appendDecoySequences(java.io.File destinationFile) throws java.io.IOException
destinationFile
- the destination file
java.io.IOException
- exception thrown whenever an error occurred while
reading or writing a filepublic void appendDecoySequences(java.io.File destinationFile, javax.swing.JProgressBar progressBar) throws java.io.IOException, java.lang.IllegalArgumentException
destinationFile
- the destination fileprogressBar
- the progress bar
java.io.IOException
- exception thrown whenever an error occurred while
reading or writing a file
java.lang.IllegalArgumentException
- exdeption thrown whenever a protein is
not foundpublic java.util.ArrayList<java.lang.String> getAccessions()
public int getnCache()
public void setnCache(int nCache)
nCache
- the new size of the cachepublic java.util.HashMap<java.lang.String,java.lang.Integer> getAAOccurrences(javax.swing.JProgressBar progressBar) throws java.io.IOException
progressBar
- a progress bar, can be null
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
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