com.compomics.util.experiment.identification

Class FastaIndex

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.FastaIndex

All Implemented Interfaces:

Serializable, Cloneable

public class FastaIndex
extends ExperimentObject

This class contains the index of a FASTA file.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
FastaIndex(HashMap<String,Long> indexes, HashSet<String> decoyAccessions, String fileName, String name, boolean concatenatedTargetDecoy, boolean isDefaultReversed, int nTarget, long lastModified, Header.DatabaseType databaseType, String decoyTag, String version) Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
Header.DatabaseType	getDatabaseType() Indicates the database type.
HashSet<String>	getDecoyAccesions() Returns the list of decoy accessions.
String	getDecoyTag() Returns the decoy tag.
static String	getDefaultVersion(long lastModified) Returns the default version based on the time the file was last modified.
String	getFileName() Returns the file name of the inspected FASTA file.
Long	getIndex(String accession) Returns the index of the accession of interest.
HashMap<String,Long>	getIndexes() Returns a map of all indexes of the FASTA file (accession -> index).
Long	getLastModified() Returns when the file was last modified.
String	getName() Returns the name of the database.
int	getNSequences() Returns the number of sequences in the database.
int	getNTarget() Returns the number of target sequences in the database.
ArrayList<String>	getSpecies() Returns the species targeted by this database.
String	getVersion() Returns the database version.
boolean	isConcatenatedTargetDecoy() Indicates whether the database is a concatenated target/decoy database.
boolean	isDecoy(String accession) Returns true if the given accession number is a decoy.
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	setConcatenatedTargetDecoy(boolean concatenatedTargetDecoy) Sets whether the database is a concatenated target/decoy database.
void	setDatabaseType(Header.DatabaseType databaseType) Sets the database type.
void	setDecoyTag(String decoyTag) Sets the decoy tag.
void	setName(String name) Sets a new name for the database.
void	setSpecies(ArrayList<String> species) Sets the species targeted by this database.
void	setVersion(String version) Sets the database version.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaIndex

public FastaIndex(HashMap<String,Long> indexes,
          HashSet<String> decoyAccessions,
          String fileName,
          String name,
          boolean concatenatedTargetDecoy,
          boolean isDefaultReversed,
          int nTarget,
          long lastModified,
          Header.DatabaseType databaseType,
          String decoyTag,
          String version)

Constructor.

Parameters:

indexes - The indexes of the inspected FASTA file

decoyAccessions - the decoy accession numbers

fileName - The FASTA file name

name - the name of the database

concatenatedTargetDecoy - If the FASTA file is a concatenated target/decoy database

isDefaultReversed - is this a default reversed database

nTarget - Number of target sequences found in the database

lastModified - a long indicating the last time the indexed file was modified

databaseType - the database type

decoyTag - the decoy tag

version - the database version

Method Detail

getIndexes

public HashMap<String,Long> getIndexes()

Returns a map of all indexes of the FASTA file (accession -> index).

Returns:

a map of all indexes of the FASTA file (accession -> index)

isDecoy

public boolean isDecoy(String accession)

Returns true if the given accession number is a decoy.

Parameters:

accession - the accession number to check

Returns:

true if the given accession number is a decoy

getDecoyAccesions

public HashSet<String> getDecoyAccesions()

Returns the list of decoy accessions.

Returns:

the list of decoy accessions

getIndex

public Long getIndex(String accession)

Returns the index of the accession of interest.

Parameters:

accession - the accession of interest

Returns:

the index of the accession of interest

getFileName

public String getFileName()

Returns the file name of the inspected FASTA file.

Returns:

the file name of the inspected FASTA file

isDefaultReversed

public boolean isDefaultReversed()

Indicates whether the decoy sequences are reversed versions of the target and the decoy accessions built based on the sequence factory methods. See getDefaultDecoyAccession(String targetAccession) in SequenceFactory.

Returns:

true if the decoy sequences are reversed versions of the target and the decoy accessions built based on the sequence factory methods

getNTarget

public int getNTarget()

Returns the number of target sequences in the database.

Returns:

the number of target sequences in the database

getNSequences

public int getNSequences()

Returns the number of sequences in the database.

Returns:

the number of sequences in the databases.

getLastModified

public Long getLastModified()

Returns when the file was last modified. Null if not set or for utilities versions older than 3.11.30.

Returns:

a long indicating when the file was last modified

getDatabaseType

public Header.DatabaseType getDatabaseType()

Indicates the database type.

Returns:

the database type.

setDatabaseType

public void setDatabaseType(Header.DatabaseType databaseType)

Sets the database type.

Parameters:

databaseType - the database type

getVersion

public String getVersion()

Returns the database version.

Returns:

the database version

setVersion

public void setVersion(String version)

Sets the database version.

Parameters:

version - the database version

isConcatenatedTargetDecoy

public boolean isConcatenatedTargetDecoy()

Indicates whether the database is a concatenated target/decoy database.

Returns:

whether the database is a concatenated target/decoy database

setConcatenatedTargetDecoy

public void setConcatenatedTargetDecoy(boolean concatenatedTargetDecoy)

Sets whether the database is a concatenated target/decoy database.

Parameters:

concatenatedTargetDecoy - whether the database is a concatenated target/decoy database

getDecoyTag

public String getDecoyTag()

Returns the decoy tag.

Returns:

sets the decoy tag

setDecoyTag

public void setDecoyTag(String decoyTag)

Sets the decoy tag.

Parameters:

decoyTag - the decoy tag

getName

public String getName()

Returns the name of the database.

Returns:

the name for the database

setName

public void setName(String name)

Sets a new name for the database.

Parameters:

name - a new name for the database

getDefaultVersion

public static String getDefaultVersion(long lastModified)

Returns the default version based on the time the file was last modified. Default version is the date "DD.MM.YYYY".

Parameters:

lastModified - long indicating when the database was last modified

Returns:

the default version

getSpecies

public ArrayList<String> getSpecies()

Returns the species targeted by this database. Note: this is not necessarily an exhaustive list of the species in the database.

Returns:

the species targeted by this database

setSpecies

public void setSpecies(ArrayList<String> species)

Sets the species targeted by this database.

Parameters:

species - the species targeted by this database