- pairwiseSequenceComp(String, String) - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
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The method performs a pairwise sequence based comparison.
- Peptide - Class in de.mpc.prolic.model
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Representation of a peptide, usually created by means of protein digestion.
- Peptide() - Constructor for class de.mpc.prolic.model.Peptide
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Empty Constructor
- Peptide(String) - Constructor for class de.mpc.prolic.model.Peptide
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- PeptideBasedComparison - Class in de.mpc.prolic.comparison
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This class provides different static methods for comparison of the peptide sets of two proteins
- PeptideBasedComparison() - Constructor for class de.mpc.prolic.comparison.PeptideBasedComparison
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- PermittedValues - Class in de.mpc.prolic.misc
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- PermittedValues() - Constructor for class de.mpc.prolic.misc.PermittedValues
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Empty constructor.
- PermittedValues(String) - Constructor for class de.mpc.prolic.misc.PermittedValues
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Constructor that creates an instance of PermittedValues for a key given in the ProLiC configuration file.
- Probe - Class in de.mpc.prolic.model
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A Probe instance is the representation of a small DNA reporter molecule that is used to measure expression levels of related transcripts and
subsequently genes by use of DNA microarray experiments.
- Probe() - Constructor for class de.mpc.prolic.model.Probe
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Empty Constructor
- Probe(String) - Constructor for class de.mpc.prolic.model.Probe
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- Probe(String, String) - Constructor for class de.mpc.prolic.model.Probe
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- Prolic - Class in de.mpc.prolic.prolic
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- Prolic(String) - Constructor for class de.mpc.prolic.prolic.Prolic
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This constructor is currently not in use.
- Prolic() - Constructor for class de.mpc.prolic.prolic.Prolic
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Empty constructor.
- ProLiCFormatException - Exception in de.mpc.prolic.exceptions
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Exception, which is thrown if the format of the input files does not fit the specifications of the ProLiC format
- ProLiCFormatException() - Constructor for exception de.mpc.prolic.exceptions.ProLiCFormatException
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Empty Constructor
- ProLiCFormatException(String) - Constructor for exception de.mpc.prolic.exceptions.ProLiCFormatException
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- ProLiCFormatException(Throwable) - Constructor for exception de.mpc.prolic.exceptions.ProLiCFormatException
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- ProLiCFormatException(String, Throwable) - Constructor for exception de.mpc.prolic.exceptions.ProLiCFormatException
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- ProLiCFormatException(String, Throwable, boolean, boolean) - Constructor for exception de.mpc.prolic.exceptions.ProLiCFormatException
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- Protein - Class in de.mpc.prolic.model
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Representation of a protein.
- Protein() - Constructor for class de.mpc.prolic.model.Protein
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Empty constructor
- Protein(String, String) - Constructor for class de.mpc.prolic.model.Protein
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The default constructor for generating instances of Protein