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Sample - Class in de.mpc.prolic.model
 
Sample() - Constructor for class de.mpc.prolic.model.Sample
Empty constructor
SequenceBasedComparison - Class in de.mpc.prolic.comparison
This class provides different static methods for comparison of two protein sequences.
SequenceBasedComparison() - Constructor for class de.mpc.prolic.comparison.SequenceBasedComparison
Empty constructor
SequenceBasedComparison(Logger) - Constructor for class de.mpc.prolic.comparison.SequenceBasedComparison
Enables logging capabilites along with creation of a SequenceBasedComparison instance
setAa_site(char) - Method in class de.mpc.prolic.model.CleavageSite
 
setBgList(ArrayList<BiomoleculeGroup>) - Method in class de.mpc.prolic.model.BiomoleculeGroupList
Stores 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)
setBiomoleculeGroup(ArrayList<Biomolecule>) - Method in class de.mpc.prolic.model.BiomoleculeGroup
 
setBiomoleculePair(Vector<Biomolecule>) - Method in class de.mpc.prolic.model.BiomoleculePair
 
setBiomolecules(ArrayList<Biomolecule>) - Method in class de.mpc.prolic.model.BiomoleculeList
 
setBiomoleculeType(String) - Method in class de.mpc.prolic.model.Biomolecule
 
setComparisonMethod(String) - Method in class de.mpc.prolic.model.BiomoleculePair
 
setComparisonResult(String) - Method in class de.mpc.prolic.model.BiomoleculePair
 
setComparisonType(String) - Method in class de.mpc.prolic.model.BiomoleculeGroup
 
setEnzymeName(String) - Method in class de.mpc.prolic.model.Enzyme
 
setGapExt(int) - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
 
setGapOpen(int) - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
 
setGeneName(String) - Method in class de.mpc.prolic.model.Protein
 
setId(Integer) - Method in class de.mpc.prolic.model.BiomoleculeGroup
 
setIdentifier(String) - Method in class de.mpc.prolic.model.Biomolecule
 
setIdentifier(String) - Method in class de.mpc.prolic.model.Sample
 
setIsN_terminalCleavage(boolean) - Method in class de.mpc.prolic.model.CleavageSite
Setter and Getter
setListIdentifier(String) - Method in class de.mpc.prolic.model.BiomoleculeGroupList
Stores a string identifier for the list of Biomolecule groups
setListName(String) - Method in class de.mpc.prolic.model.BiomoleculeList
 
setLog4j(Logger) - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
 
setOrigin(String) - Method in class de.mpc.prolic.model.Biomolecule
 
setPeptides(ArrayList<Peptide>) - Method in class de.mpc.prolic.model.Protein
 
setPerformsN_terminalCleavage(boolean) - Method in class de.mpc.prolic.model.Enzyme
 
setPidMethod(String) - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
Setter and getter
setProbes(ArrayList<Probe>) - Method in class de.mpc.prolic.model.Transcript
 
setProteinName(String) - Method in class de.mpc.prolic.model.Protein
 
setRegExDigestion(String) - Method in class de.mpc.prolic.model.Enzyme
 
setRegulation(double) - Method in class de.mpc.prolic.model.Biomolecule
 
setRegulation(double) - Method in class de.mpc.prolic.model.Sample
 
setRelatedProt(Protein) - Method in class de.mpc.prolic.model.Peptide
 
setRelatedProt(Transcript) - Method in class de.mpc.prolic.model.Probe
 
setRelatedProt(Gene) - Method in class de.mpc.prolic.model.Transcript
 
setRepresentative(Biomolecule) - Method in class de.mpc.prolic.model.BiomoleculeGroup
 
setSequence(String) - Method in class de.mpc.prolic.model.Biomolecule
 
setSequenceComparisonScore(double) - Method in class de.mpc.prolic.model.BiomoleculePair
 
setSubstMatrixID(String) - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
 
setTranscripts(ArrayList<Transcript>) - Method in class de.mpc.prolic.model.Gene
 
setUniqueIdentifier(String) - Method in class de.mpc.prolic.model.Biomolecule
 
sortBiomoleculeGroups() - Method in class de.mpc.prolic.model.BiomoleculeGroupList
Sorts all BiomoleculeGroup
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