Package | Description |
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.identification.protein_sequences |
Protein sequence handling related classes.
|
com.compomics.util.protein |
Classes concerning useful Objects and their operations for modeling and handling proteins.
|
Modifier and Type | Method and Description |
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Header.DatabaseType |
Protein.getDatabaseType()
Getter for the protein database type.
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Constructor and Description |
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Protein(String accession,
Header.DatabaseType databaseType,
String sequence,
boolean isDecoy)
Constructor for a protein.
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Modifier and Type | Method and Description |
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Header.DatabaseType |
FastaIndex.getMainDatabaseType()
Returns the main database type.
|
Modifier and Type | Method and Description |
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HashMap<Header.DatabaseType,Integer> |
FastaIndex.getDatabaseTypes()
Returns the map of the database types and how often they occur.
|
Modifier and Type | Method and Description |
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void |
FastaIndex.setMainDatabaseType(Header.DatabaseType mainDatabaseType)
Sets the main database type.
|
Modifier and Type | Method and Description |
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void |
FastaIndex.setDatabaseTypes(HashMap<Header.DatabaseType,Integer> databaseTypes)
Set the database types map.
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Constructor and Description |
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FastaIndex(HashMap<String,Long> indexes,
HashSet<String> decoyAccessions,
String fileName,
String name,
boolean concatenatedTargetDecoy,
boolean isDefaultReversed,
int nTarget,
long lastModified,
Header.DatabaseType mainDatabaseType,
HashMap<Header.DatabaseType,Integer> databaseTypes,
String decoyTag,
String version,
HashMap<String,Integer> speciesOccurrence)
Constructor.
|
Constructor and Description |
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FastaIndex(HashMap<String,Long> indexes,
HashSet<String> decoyAccessions,
String fileName,
String name,
boolean concatenatedTargetDecoy,
boolean isDefaultReversed,
int nTarget,
long lastModified,
Header.DatabaseType mainDatabaseType,
HashMap<Header.DatabaseType,Integer> databaseTypes,
String decoyTag,
String version,
HashMap<String,Integer> speciesOccurrence)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
Header.DatabaseType |
Header.getDatabaseType() |
static Header.DatabaseType |
Header.DatabaseType.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static Header.DatabaseType[] |
Header.DatabaseType.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
static String |
Header.getDatabaseTypeAsString(Header.DatabaseType databaseType)
Convenience method returning the database name as a String.
|
void |
Header.setDatabaseType(Header.DatabaseType aDatabaseType) |
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