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bilateralCompPeptOnly(Protein, Protein) - Static method in class de.mpc.prolic.comparison.PeptideBasedComparison
Performs a peptide based comparison that considers only the available peptide sets of the two proteins specified.
bilateralCompPeptSeq(Protein, Protein, ArrayList<Enzyme>) - Static method in class de.mpc.prolic.comparison.PeptideBasedComparison
Performs a peptide based comparison of two proteins obtained from different protein list.
bilateralCompPeptSeqMod(Protein, Protein, ArrayList<Enzyme>) - Static method in class de.mpc.prolic.comparison.PeptideBasedComparison
Performs a peptide based comparison of two proteins obtained from different protein lists.
Biomolecule - Class in de.mpc.prolic.model
The superclass for all biological molecules that contain sequence information.
Biomolecule() - Constructor for class de.mpc.prolic.model.Biomolecule
Empty constructor
Biomolecule(String) - Constructor for class de.mpc.prolic.model.Biomolecule
For biomolecules that are part of higher level entities (e.g. peptides that are associated with their bearing proteins) Here, the information about the origin is stored as part of the higher level entity.
Biomolecule(String, String) - Constructor for class de.mpc.prolic.model.Biomolecule
The default constructor for generating instances of Biomolecule
BiomoleculeGroup - Class in de.mpc.prolic.model
 
BiomoleculeGroup() - Constructor for class de.mpc.prolic.model.BiomoleculeGroup
Empty constructor
BiomoleculeGroup(String) - Constructor for class de.mpc.prolic.model.BiomoleculeGroup
Specification of the comparison method applied is given with the creation of the BiomoleculeGroup instance
BiomoleculeGroupList - Class in de.mpc.prolic.model
This Class stores a sorted set of related biomolecule groups obtained from comparison (i.e. the BiomleculeGroupList represents either an intersection or the set differences)
BiomoleculeGroupList() - Constructor for class de.mpc.prolic.model.BiomoleculeGroupList
Empty constructor
BiomoleculeList - Class in de.mpc.prolic.model
 
BiomoleculeList() - Constructor for class de.mpc.prolic.model.BiomoleculeList
Empty constructor
BiomoleculeList(ArrayList<Biomolecule>) - Constructor for class de.mpc.prolic.model.BiomoleculeList
Generating a BiomoleculeList instance along with a collection of the related biomolecules.
BiomoleculeList(ArrayList<Biomolecule>, String) - Constructor for class de.mpc.prolic.model.BiomoleculeList
Generating a BiomoleculeList instance along with a collection of the related biomolecules and the list identifier.
BiomoleculePair - Class in de.mpc.prolic.model
This class encapsulates a set of two biomolecules that pass the test for identity along with the utilized comaparison method, the score obtained from a sequence based comparison and a string representation of the comparison result in case of a sequence based comparison (i.e. the aligned strings and an identification of the aligned positions and the existing gaps etc.)
BiomoleculePair() - Constructor for class de.mpc.prolic.model.BiomoleculePair
 
buildListIdentifier(BiomoleculeGroup) - Static method in class de.mpc.prolic.misc.Tools
Building a list identifier for this BiomoleculeGroup
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