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java.lang.Objectcom.compomics.util.experiment.identification.SequenceFactory
public class SequenceFactory
Factory retrieving the information of the loaded FASTA file.
Method Summary | |
---|---|
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. |
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(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. |
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 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. |
void |
setnCache(int nCache)
Sets the size of the cache. |
static void |
setTargetDecoyFileNameTag(String targetDecoyFileNameTag)
Set the target-decoy file name tag. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static SequenceFactory getInstance()
public static SequenceFactory getInstance(int nCache)
nCache
- the new cache size
public void clearFactory() throws IOException, SQLException
IOException
SQLException
public void emptyCache()
public Protein getProtein(String accession) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
accession
- accession of the desired protein
IOException
- thrown whenever an error is encountered while reading
the FASTA file
IllegalArgumentException
- thrown whenever an error is encountered
while reading the FASTA file
InterruptedException
FileNotFoundException
ClassNotFoundException
public Header getHeader(String accession) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
accession
- accession of the desired protein
IOException
- exception thrown whenever an error occurred while
reading the FASTA file
IllegalArgumentException
- exception thrown whenever a protein is
not found
InterruptedException
FileNotFoundException
ClassNotFoundException
public void loadFastaFile(File fastaFile) throws FileNotFoundException, IOException, ClassNotFoundException, StringIndexOutOfBoundsException, IllegalArgumentException
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 index
StringIndexOutOfBoundsException
- thrown if issues occur during the
parsing of the protein headers
IllegalArgumentException
- 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 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 index
StringIndexOutOfBoundsException
- thrown if issues occur during the
parsing of the protein headers
IllegalArgumentException
- if non unique accession numbers are
foundpublic void saveIndex() throws IOException
IOException
public void closeFile() throws IOException, SQLException
IOException
- exception thrown whenever an error occurred while
closing the file
SQLException
public static boolean isDecoy(String proteinAccession, String decoyFlag)
proteinAccession
- The accession of the proteindecoyFlag
- the decoy flag
public static String getDecoyFlag(String proteinAccession)
proteinAccession
- the protein accession
public boolean isDecoyAccession(String proteinAccession)
proteinAccession
- the protein accession of interest.
public static boolean isDecoy(String proteinAccession)
proteinAccession
- the accession of interest
public boolean concatenatedTargetDecoy()
public boolean isDefaultReversed()
public int getNTargetSequences()
public void appendDecoySequences(File destinationFile) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
destinationFile
- the destination file
IOException
- exception thrown whenever an error occurred while
reading or writing a file
IllegalArgumentException
InterruptedException
FileNotFoundException
ClassNotFoundException
public void appendDecoySequences(File destinationFile, WaitingHandler waitingHandler) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
destinationFile
- the destination filewaitingHandler
- the waiting handler
IOException
- exception thrown whenever an error occurred while
reading or writing a file
IllegalArgumentException
- exception thrown whenever a protein is
not found
InterruptedException
FileNotFoundException
ClassNotFoundException
public static String reverseSequence(String sequence)
sequence
- the protein sequence
public 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 null
IOException
- exception thrown whenever an error occurred while
reading the database
IllegalArgumentException
InterruptedException
FileNotFoundException
ClassNotFoundException
public double computeMolecularWeight(String accession) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
accession
- the protein's accession number
IOException
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 accession
public static String getDefaultDecoyDescription(String targetDescription)
targetDescription
- the description of a target protein
public static String getDefaultTargetAccession(String decoyAccession)
decoyAccession
- the decoy accession
public FastaIndex getCurrentFastaIndex()
public ProteinTree getDefaultProteinTree() throws IOException, InterruptedException, ClassNotFoundException, IllegalArgumentException, SQLException
IOException
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 tree
IOException
InterruptedException
ClassNotFoundException
IllegalArgumentException
SQLException
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