com.compomics.util.protein_sequences_manager

Class ProteinSequencesManager

java.lang.Object

com.compomics.util.protein_sequences_manager.ProteinSequencesManager

public class ProteinSequencesManager
extends Object

The protein sequences manager helps the user manage FASTA files.

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
static String	DNA_FOLDER Name of the folder containing DNA translated files.
static String	TEMP_FOLDER Name of the folder containing temporary files.
static String	UNIPROT_FOLDER Name of the folder containing UniProt files.
static String	USER_FOLDER Name of the folder containing user FASTA files.

Constructor Summary

Constructors

Constructor and Description
ProteinSequencesManager() Constructor.

Method Summary

Modifier and Type	Method and Description
void	addFastaFile(File fastaFile, SequenceInputType sequenceInputType, WaitingHandler waitingHandler) Adds a FASTA file to the working folder.
static String	correctFastaName(String fastaName) Corrects the name of the given FASTA file.
ArrayList<String>	getDatabaseNames() Returns the list of database names parsed from the working folder.
File	getDnaFolder() Returns the folder where DNA databases are stored.
FastaIndex	getFastaIndex(String databaseName, String version) Returns the FASTA index of the given database name and version.
File	getFolder(SequenceInputType sequenceInputType) Returns the folder to be used for the given input type.
SequenceInputType	getInputType(String databaseName) Returns the input type of the given database.
File	getTempFolder() Returns the temporary folder.
File	getUniprotFolder() Returns the folder where UniProt databases are stored.
File	getUserFolder() Returns the folder where user databases are stored.
ArrayList<String>	getVersionsForDb(String databaseName) Returns the list of versions for the given database name as parsed from the working folder.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

TEMP_FOLDER

public static final String TEMP_FOLDER

Name of the folder containing temporary files.

See Also:

Constant Field Values

UNIPROT_FOLDER

public static final String UNIPROT_FOLDER

Name of the folder containing UniProt files.

See Also:

Constant Field Values

USER_FOLDER

public static final String USER_FOLDER

Name of the folder containing user FASTA files.

See Also:

Constant Field Values

DNA_FOLDER

public static final String DNA_FOLDER

Name of the folder containing DNA translated files.

See Also:

Constant Field Values

Constructor Detail

ProteinSequencesManager

public ProteinSequencesManager()

Constructor. The Protein Sequences Manager folder must be set in the utilities preferences before calling the constructor.

Method Detail

getUniprotFolder

public File getUniprotFolder()

Returns the folder where UniProt databases are stored.

Returns:

the folder where UniProt databases are stored

getUserFolder

public File getUserFolder()

Returns the folder where user databases are stored.

Returns:

the folder where user databases are stored

getDnaFolder

public File getDnaFolder()

Returns the folder where DNA databases are stored.

Returns:

the folder where DNA databases are stored

addFastaFile

public void addFastaFile(File fastaFile,
                         SequenceInputType sequenceInputType,
                         WaitingHandler waitingHandler)
                  throws IOException

Adds a FASTA file to the working folder.

Parameters:

fastaFile - the FASTA file to add

sequenceInputType - the type of input

waitingHandler - a waiting handler displaying progress and allowing canceling the operation.

Throws:

IOException - exception thrown whenever an error occurred while copying the file.

correctFastaName

public static String correctFastaName(String fastaName)

Corrects the name of the given FASTA file.

Parameters:

fastaName - the name of the given FASTA file

Returns:

a corrected name for the given FASTA file

getFolder

public File getFolder(SequenceInputType sequenceInputType)

Returns the folder to be used for the given input type.

Parameters:

sequenceInputType - the type of input

Returns:

the folder to be used for the given input type

getTempFolder

public File getTempFolder()

Returns the temporary folder.

Returns:

the temporary folder

getDatabaseNames

public ArrayList<String> getDatabaseNames()

Returns the list of database names parsed from the working folder.

Returns:

the list of database names parsed from the working folder

getVersionsForDb

public ArrayList<String> getVersionsForDb(String databaseName)

Returns the list of versions for the given database name as parsed from the working folder.

Parameters:

databaseName - the name of the database of interest

Returns:

the list of versions for the given database name as parsed from the working folder

getFastaIndex

public FastaIndex getFastaIndex(String databaseName,
                                String version)

Returns the FASTA index of the given database name and version.

Parameters:

databaseName - the name of the database of interest

version - the version of the database of interest

Returns:

the corresponding FASTA index

getInputType

public SequenceInputType getInputType(String databaseName)

Returns the input type of the given database.

Parameters:

databaseName - the name of the database

Returns:

the input type of the given database