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