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P

pairwiseSequenceComp(String, String) - Method in class de.mpc.prolic.comparison.SequenceBasedComparison
The method performs a pairwise sequence based comparison.
Peptide - Class in de.mpc.prolic.model
Representation of a peptide, usually created by means of protein digestion.
Peptide() - Constructor for class de.mpc.prolic.model.Peptide
Empty Constructor
Peptide(String) - Constructor for class de.mpc.prolic.model.Peptide
 
PeptideBasedComparison - Class in de.mpc.prolic.comparison
This class provides different static methods for comparison of the peptide sets of two proteins
PeptideBasedComparison() - Constructor for class de.mpc.prolic.comparison.PeptideBasedComparison
 
PermittedValues - Class in de.mpc.prolic.misc
 
PermittedValues() - Constructor for class de.mpc.prolic.misc.PermittedValues
Empty constructor.
PermittedValues(String) - Constructor for class de.mpc.prolic.misc.PermittedValues
Constructor that creates an instance of PermittedValues for a key given in the ProLiC configuration file.
Probe - Class in de.mpc.prolic.model
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
Empty Constructor
Probe(String) - Constructor for class de.mpc.prolic.model.Probe
 
Probe(String, String) - Constructor for class de.mpc.prolic.model.Probe
 
Prolic - Class in de.mpc.prolic.prolic
 
Prolic(String) - Constructor for class de.mpc.prolic.prolic.Prolic
This constructor is currently not in use.
Prolic() - Constructor for class de.mpc.prolic.prolic.Prolic
Empty constructor.
ProLiCFormatException - Exception in de.mpc.prolic.exceptions
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
Empty Constructor
ProLiCFormatException(String) - Constructor for exception de.mpc.prolic.exceptions.ProLiCFormatException
 
ProLiCFormatException(Throwable) - Constructor for exception de.mpc.prolic.exceptions.ProLiCFormatException
 
ProLiCFormatException(String, Throwable) - Constructor for exception de.mpc.prolic.exceptions.ProLiCFormatException
 
ProLiCFormatException(String, Throwable, boolean, boolean) - Constructor for exception de.mpc.prolic.exceptions.ProLiCFormatException
 
Protein - Class in de.mpc.prolic.model
Representation of a protein.
Protein() - Constructor for class de.mpc.prolic.model.Protein
Empty constructor
Protein(String, String) - Constructor for class de.mpc.prolic.model.Protein
The default constructor for generating instances of Protein
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