Uses of Enum
com.compomics.util.experiment.io.biology.protein.ProteinDatabase

Packages that use ProteinDatabase

Package	Description
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.io.biology.protein	Experiment IO classes for biological resources.

Uses of ProteinDatabase in com.compomics.util.experiment.identification.protein_inference.fm_index

Methods in com.compomics.util.experiment.identification.protein_inference.fm_index that return ProteinDatabase

Modifier and Type	Method	Description
ProteinDatabase	FMIndex.getProteinDatabase(String proteinAccession)

Uses of ProteinDatabase in com.compomics.util.experiment.io.biology.protein

Fields in com.compomics.util.experiment.io.biology.protein with type parameters of type ProteinDatabase

Modifier and Type	Field	Description
final HashMap<ProteinDatabase,Integer>	FastaSummary.databaseType	The database type occurrence in the FASTA file.

Methods in com.compomics.util.experiment.io.biology.protein that return ProteinDatabase

Modifier and Type	Method	Description
ProteinDatabase	Header.getDatabaseType()	Returns the database type as inferred from the header structure.
ProteinDatabase	ProteinDatabase.getProteinDatabase(String fullName)	Returns the protein database with the given full name, null if not found.
ProteinDatabase	ProteinDetailsProvider.getProteinDatabase(String accession)	Returns the the protein database for the given protein.
static ProteinDatabase	ProteinDatabase.valueOf(String name)	Returns the enum constant of this type with the specified name.
static ProteinDatabase[]	ProteinDatabase.values()	Returns an array containing the constants of this enum type, in the order they are declared.

Methods in com.compomics.util.experiment.io.biology.protein with parameters of type ProteinDatabase

Modifier and Type	Method	Description
static String	Header.getDatabaseTypeAsString(ProteinDatabase databaseType)	Convenience method returning the database name as a String.
void	Header.setDatabaseType(ProteinDatabase aDatabaseType)	Sets the database type.

Constructor parameters in com.compomics.util.experiment.io.biology.protein with type arguments of type ProteinDatabase

Modifier	Constructor	Description
	FastaSummary(String name, String description, String version, File fastaFile, TreeMap<String,Integer> speciesOccurrence, HashMap<ProteinDatabase,Integer> databaseType, int nSequences, int nTarget, long lastModified)	Constructor.