- calcMaxNumberPeptids(BiomoleculeList) - Static method in class de.mpc.prolic.misc.Tools
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Calculates the maximum number of peptides that are assigned to a protein within the given BiomoleculeList.
- calculateExternalGaps(String) - Static method in class de.mpc.prolic.misc.Tools
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Calculates the number of terminal gaps for the given string that represents the result of a pairwise sequence alignment.
- calculateNumberGaps(String) - Method in class de.mpc.prolic.misc.Tools
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The method calculates the number of gaps for a given sequence obtained for an alignment algorithm
- checkCleavageSite(char) - Method in class de.mpc.prolic.model.Enzyme
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The method checks whether the enzyme has a specific cleavage site
- checkCompleteConfigurationFile() - Method in class de.mpc.prolic.misc.CheckConfiguration
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The method validates all the values given in the ProLiC configuration file.
- CheckConfiguration - Class in de.mpc.prolic.misc
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- CheckConfiguration(String) - Constructor for class de.mpc.prolic.misc.CheckConfiguration
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Empty constructor
- CleavageSite - Class in de.mpc.prolic.model
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Represents a cleavage site of an enzyme.
- CleavageSite() - Constructor for class de.mpc.prolic.model.CleavageSite
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Empty constructor
- compareTo(Object) - Method in class de.mpc.prolic.misc.ListIdentifier
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- compareTo(Object) - Method in class de.mpc.prolic.model.Biomolecule
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- compareTo(Object) - Method in class de.mpc.prolic.model.BiomoleculeGroup
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- compareTo(Object) - Method in class de.mpc.prolic.model.BiomoleculeGroupList
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- createEnzyme(String) - Static method in class de.mpc.prolic.misc.Tools
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This method creates an instance of Enzyme from the information specified in the Enzymes section of the configuration file.