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G

Gene - Class in de.mpc.prolic.model
Representation of a Gene.
Gene() - Constructor for class de.mpc.prolic.model.Gene
Empty Constructor
Gene(String, String) - Constructor for class de.mpc.prolic.model.Gene
 
getAa_site() - Method in class de.mpc.prolic.model.CleavageSite
 
getAppliedDefaultValues() - Method in class de.mpc.prolic.misc.CheckConfiguration
The method returns a Map with key-value pairs where a) wrong settings have been applied in the ProLiC configuration file and b) default values are applied in order to prevent ProLiC from shutdown.
getBgList() - Method in class de.mpc.prolic.model.BiomoleculeGroupList
Retrieves a list of biomolecule groups (i.e. a representation of related biomolecules, which are member of either a set difference or an intersection considering a set of compared biomolecule lists)
getBiomoleculeGroup() - Method in class de.mpc.prolic.model.BiomoleculeGroup
 
getBiomoleculePair() - Method in class de.mpc.prolic.model.BiomoleculePair
Setter and Getter
getBiomolecules() - Method in class de.mpc.prolic.model.BiomoleculeList
 
getBiomoleculeType() - Method in class de.mpc.prolic.model.Biomolecule
 
getCleavageSites() - Method in class de.mpc.prolic.model.Enzyme
Setter and Getter
getComparisonMethod() - Method in class de.mpc.prolic.model.BiomoleculePair
 
getComparisonResult() - Method in class de.mpc.prolic.model.BiomoleculePair
 
getComparisonType() - Method in class de.mpc.prolic.model.BiomoleculeGroup
Setter and Getter
getCurrentDate() - Static method in class de.mpc.prolic.misc.Tools
Gives a formatted string representation of the current date and time.
getDebugMode() - Method in class de.mpc.prolic.prolic.Prolic
 
getEnzymeName() - Method in class de.mpc.prolic.model.Enzyme
 
getEnzymes() - Method in class de.mpc.prolic.model.Digest
Setter and Getter
getFileExtension(String) - Static method in class de.mpc.prolic.misc.Tools
Gets the extension from the specified name of the file.
getGapExt() - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
 
getGapOpen() - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
 
getGeneName() - Method in class de.mpc.prolic.model.Protein
 
getId() - Method in class de.mpc.prolic.model.BiomoleculeGroup
 
getIdentifier() - Method in class de.mpc.prolic.model.Biomolecule
 
getIdentifier() - Method in class de.mpc.prolic.model.Sample
Setter and Getter
getInconsistenciesExist() - Method in class de.mpc.prolic.prolic.Prolic
Setter and Getter
getIsN_terminalCleavage() - Method in class de.mpc.prolic.model.CleavageSite
 
getKey() - Method in class de.mpc.prolic.misc.PermittedValues
 
getListIdentifier() - Method in class de.mpc.prolic.misc.ListIdentifier
 
getListIdentifier() - Method in class de.mpc.prolic.model.BiomoleculeGroupList
The method retrieves a string identifier for the list of Biomolecule groups
getListName() - Method in class de.mpc.prolic.model.BiomoleculeList
Setter and Getter
getMap() - Method in class de.mpc.prolic.misc.IniReader
This method returns the Map structure that gives for each key (= section name of the ini file) a Map that consists of further key-value pairs (configuration parameters)
getOrigin() - Method in class de.mpc.prolic.model.Biomolecule
 
getPeptides() - Method in class de.mpc.prolic.model.Protein
 
getPerformsN_terminalCleavage() - Method in class de.mpc.prolic.model.Enzyme
 
getPermittedValues() - Method in class de.mpc.prolic.misc.PermittedValues
 
getPidMethod() - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
 
getProbes() - Method in class de.mpc.prolic.model.Transcript
 
getPropertyBool(String, String, boolean) - Method in class de.mpc.prolic.misc.IniReader
This method returns a specific boolean value stored in an ini-File with respect to a given section and a key
getPropertyInt(String, String, int) - Method in class de.mpc.prolic.misc.IniReader
This method returns a specific integer value stored in an ini-File with respect to a given section and a key
getPropertyString(String, String, String) - Method in class de.mpc.prolic.misc.IniReader
This method returns a specific string value stored in an ini-File with respect to a given section and a key
getProteinName() - Method in class de.mpc.prolic.model.Protein
Setter and Getter
getProtSeqTarget(String) - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
Method is necessary for determination that the target sequence causes the exception.
getRegExDigestion() - Method in class de.mpc.prolic.model.Enzyme
 
getRegulation() - Method in class de.mpc.prolic.model.Biomolecule
 
getRegulation() - Method in class de.mpc.prolic.model.Sample
 
getRelatedGene() - Method in class de.mpc.prolic.model.Transcript
Setter and Getter
getRelatedProt() - Method in class de.mpc.prolic.model.Peptide
Setter and Getter
getRelatedTranscript() - Method in class de.mpc.prolic.model.Probe
Setter and Getter
getRepresentative() - Method in class de.mpc.prolic.model.BiomoleculeGroup
 
getSequence() - Method in class de.mpc.prolic.model.Biomolecule
Setter and Getter
getSequenceComparisonScore() - Method in class de.mpc.prolic.model.BiomoleculePair
 
getSubstMatrixID() - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
 
getTranscripts() - Method in class de.mpc.prolic.model.Gene
Setter and Getter
getUniqueIdentifier() - Method in class de.mpc.prolic.model.Biomolecule
 
getWrongValues() - Method in class de.mpc.prolic.misc.CheckConfiguration
The method returns a Map with key-value pairs where wrong settings have been applied in the ProLiC configuration file.
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