- ReadIniSectionException - Exception in de.mpc.prolic.exceptions
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Exception, which is thrown if problems occur while accessing the ProLiC configuration file
- ReadIniSectionException() - Constructor for exception de.mpc.prolic.exceptions.ReadIniSectionException
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Empty Constructor
- ReadIniSectionException(String) - Constructor for exception de.mpc.prolic.exceptions.ReadIniSectionException
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- ReadIniSectionException(Throwable) - Constructor for exception de.mpc.prolic.exceptions.ReadIniSectionException
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- ReadIniSectionException(String, Throwable) - Constructor for exception de.mpc.prolic.exceptions.ReadIniSectionException
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- ReadIniSectionException(String, Throwable, boolean, boolean) - Constructor for exception de.mpc.prolic.exceptions.ReadIniSectionException
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- readProLiCformatedProteinFile(File, String, String, boolean, boolean, Logger, Boolean) - Static method in class de.mpc.prolic.misc.IO
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Reads protein data (including the related peptide information) from a file in the ProLiC format and builds the protein instances.
- readSectionFromIni(String, String, Boolean, String, boolean) - Static method in class de.mpc.prolic.misc.IO
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Reading the settings for ProLiC from a specific section of the configuration file.
- removeModifications(String, String) - Static method in class de.mpc.prolic.misc.Tools
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Removes the modification information from a given sequence with respect to the applied notation of modifications.
- removeModificationsFromPeptideSet(ArrayList<Peptide>, String) - Static method in class de.mpc.prolic.misc.Tools
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Removes the modification information from all peptides in a given peptide set.
- removePTMs(String, String) - Static method in class de.mpc.prolic.misc.Tools
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Removes the modification information from a given sequence.