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