- 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