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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Modifier and Type | Method and Description |
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ProteinDatabase |
FMIndex.getProteinDatabase(String accession) |
Modifier and Type | Field and Description |
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HashMap<ProteinDatabase,Integer> |
FastaSummary.databaseType
The database type occurrence in the FASTA file.
|
Modifier and Type | Method and Description |
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ProteinDatabase |
Header.getDatabaseType()
Returns the database type as inferred from the header structure.
|
ProteinDatabase |
ProteinDetailsProvider.getProteinDatabase(String accession)
Returns the the protein database for the given protein.
|
ProteinDatabase |
ProteinDatabase.getProteinDatabase(String fullName)
Returns the protein database with the given full name, null if not found.
|
static ProteinDatabase |
ProteinDatabase.valueOf(String name)
Returns the enum constant of this type with the specified name.
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static ProteinDatabase[] |
ProteinDatabase.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
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Modifier and Type | Method and Description |
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static String |
Header.getDatabaseTypeAsString(ProteinDatabase databaseType)
Convenience method returning the database name as a String.
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void |
Header.setDatabaseType(ProteinDatabase aDatabaseType)
Sets the database type.
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Constructor and Description |
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FastaSummary(String name,
String description,
String version,
File fastaFile,
TreeMap<String,Integer> speciesOccurrence,
HashMap<ProteinDatabase,Integer> databaseType,
int nSequences,
int nTarget,
long lastModified)
Constructor.
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