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C

calcMaxNumberPeptids(BiomoleculeList) - Static method in class de.mpc.prolic.misc.Tools
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
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
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
The method checks whether the enzyme has a specific cleavage site
checkCompleteConfigurationFile() - Method in class de.mpc.prolic.misc.CheckConfiguration
The method validates all the values given in the ProLiC configuration file.
CheckConfiguration - Class in de.mpc.prolic.misc
 
CheckConfiguration(String) - Constructor for class de.mpc.prolic.misc.CheckConfiguration
Empty constructor
CleavageSite - Class in de.mpc.prolic.model
Represents a cleavage site of an enzyme.
CleavageSite() - Constructor for class de.mpc.prolic.model.CleavageSite
Empty constructor
compareTo(Object) - Method in class de.mpc.prolic.misc.ListIdentifier
 
compareTo(Object) - Method in class de.mpc.prolic.model.Biomolecule
 
compareTo(Object) - Method in class de.mpc.prolic.model.BiomoleculeGroup
 
compareTo(Object) - Method in class de.mpc.prolic.model.BiomoleculeGroupList
 
createEnzyme(String) - Static method in class de.mpc.prolic.misc.Tools
This method creates an instance of Enzyme from the information specified in the Enzymes section of the configuration file.
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