- Gene - Class in de.mpc.prolic.model
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Representation of a Gene.
- Gene() - Constructor for class de.mpc.prolic.model.Gene
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Empty Constructor
- Gene(String, String) - Constructor for class de.mpc.prolic.model.Gene
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- getAa_site() - Method in class de.mpc.prolic.model.CleavageSite
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- getAppliedDefaultValues() - Method in class de.mpc.prolic.misc.CheckConfiguration
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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
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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
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- getBiomoleculePair() - Method in class de.mpc.prolic.model.BiomoleculePair
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Setter and Getter
- getBiomolecules() - Method in class de.mpc.prolic.model.BiomoleculeList
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- getBiomoleculeType() - Method in class de.mpc.prolic.model.Biomolecule
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- getCleavageSites() - Method in class de.mpc.prolic.model.Enzyme
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Setter and Getter
- getComparisonMethod() - Method in class de.mpc.prolic.model.BiomoleculePair
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- getComparisonResult() - Method in class de.mpc.prolic.model.BiomoleculePair
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- getComparisonType() - Method in class de.mpc.prolic.model.BiomoleculeGroup
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Setter and Getter
- getCurrentDate() - Static method in class de.mpc.prolic.misc.Tools
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Gives a formatted string representation of the current date and time.
- getDebugMode() - Method in class de.mpc.prolic.prolic.Prolic
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- getEnzymeName() - Method in class de.mpc.prolic.model.Enzyme
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- getEnzymes() - Method in class de.mpc.prolic.model.Digest
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Setter and Getter
- getFileExtension(String) - Static method in class de.mpc.prolic.misc.Tools
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Gets the extension from the specified name of the file.
- getGapExt() - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
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- getGapOpen() - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
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- getGeneName() - Method in class de.mpc.prolic.model.Protein
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- getId() - Method in class de.mpc.prolic.model.BiomoleculeGroup
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- getIdentifier() - Method in class de.mpc.prolic.model.Biomolecule
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- getIdentifier() - Method in class de.mpc.prolic.model.Sample
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Setter and Getter
- getInconsistenciesExist() - Method in class de.mpc.prolic.prolic.Prolic
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Setter and Getter
- getIsN_terminalCleavage() - Method in class de.mpc.prolic.model.CleavageSite
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- getKey() - Method in class de.mpc.prolic.misc.PermittedValues
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- getListIdentifier() - Method in class de.mpc.prolic.misc.ListIdentifier
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- getListIdentifier() - Method in class de.mpc.prolic.model.BiomoleculeGroupList
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The method retrieves a string identifier for the list of Biomolecule groups
- getListName() - Method in class de.mpc.prolic.model.BiomoleculeList
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Setter and Getter
- getMap() - Method in class de.mpc.prolic.misc.IniReader
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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
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- getPeptides() - Method in class de.mpc.prolic.model.Protein
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- getPerformsN_terminalCleavage() - Method in class de.mpc.prolic.model.Enzyme
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- getPermittedValues() - Method in class de.mpc.prolic.misc.PermittedValues
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- getPidMethod() - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
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- getProbes() - Method in class de.mpc.prolic.model.Transcript
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- getPropertyBool(String, String, boolean) - Method in class de.mpc.prolic.misc.IniReader
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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
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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
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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
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Setter and Getter
- getProtSeqTarget(String) - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
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Method is necessary for determination that the target sequence causes the exception.
- getRegExDigestion() - Method in class de.mpc.prolic.model.Enzyme
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- getRegulation() - Method in class de.mpc.prolic.model.Biomolecule
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- getRegulation() - Method in class de.mpc.prolic.model.Sample
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- getRelatedGene() - Method in class de.mpc.prolic.model.Transcript
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Setter and Getter
- getRelatedProt() - Method in class de.mpc.prolic.model.Peptide
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Setter and Getter
- getRelatedTranscript() - Method in class de.mpc.prolic.model.Probe
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Setter and Getter
- getRepresentative() - Method in class de.mpc.prolic.model.BiomoleculeGroup
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- getSequence() - Method in class de.mpc.prolic.model.Biomolecule
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Setter and Getter
- getSequenceComparisonScore() - Method in class de.mpc.prolic.model.BiomoleculePair
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- getSubstMatrixID() - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
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- getTranscripts() - Method in class de.mpc.prolic.model.Gene
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Setter and Getter
- getUniqueIdentifier() - Method in class de.mpc.prolic.model.Biomolecule
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- getWrongValues() - Method in class de.mpc.prolic.misc.CheckConfiguration
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The method returns a Map with key-value pairs where wrong settings have been
applied in the ProLiC configuration file.