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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,
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(java.lang.String accession)
Returns the protein's molecular weight. |
boolean |
concatenatedTargetDecoy()
Indicates whether the database loaded contains decoy sequences. |
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. |
Header |
getHeader(java.lang.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(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,
WaitingHandler waitingHandler)
Loads a new FASTA file in the factory. |
void |
setnCache(int nCache)
Sets the size of the cache. |
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 void clearFactory()
public Protein getProtein(java.lang.String accession) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException
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 file
java.lang.InterruptedException
public Header getHeader(java.lang.String accession) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException
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 found
java.lang.InterruptedException
public 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, WaitingHandler waitingHandler) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException, java.lang.StringIndexOutOfBoundsException
fastaFile
- the FASTA file to loadwaitingHandler
- a waitingHandler 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 index
java.lang.StringIndexOutOfBoundsException
- thrown if issues occur during the parsing of the protein headerspublic void closeFile() throws java.io.IOException
java.io.IOException
- exception thrown whenever an error occurred while
closing 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, java.lang.IllegalArgumentException, java.lang.InterruptedException, java.io.FileNotFoundException, java.lang.ClassNotFoundException
destinationFile
- the destination file
java.io.IOException
- exception thrown whenever an error occurred while
reading or writing a file
java.lang.IllegalArgumentException
java.lang.InterruptedException
java.io.FileNotFoundException
java.lang.ClassNotFoundException
public void appendDecoySequences(java.io.File destinationFile, WaitingHandler waitingHandler) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException, java.io.FileNotFoundException, java.lang.ClassNotFoundException
destinationFile
- the destination filewaitingHandler
- the waiting handler
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 found
java.lang.InterruptedException
java.io.FileNotFoundException
java.lang.ClassNotFoundException
public 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, java.lang.IllegalArgumentException, java.lang.InterruptedException
progressBar
- a progress bar, can be null
java.io.IOException
- exception thrown whenever an error occurred while
reading the database
java.lang.IllegalArgumentException
java.lang.InterruptedException
public double computeMolecularWeight(java.lang.String accession) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException
accession
- the protein's accession number
java.io.IOException
java.lang.IllegalArgumentException
java.lang.InterruptedException
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