JPL-Core 1.0 API Documentation

Packages

org.expasy.jpl.core.mol	Here are definitions and descriptions of simple chemical and complex molecular objects such as amino-acids or biological polymers.
org.expasy.jpl.core.mol.chem	Here lies atoms, isotopes, builders, managers and facades that handle their access.
org.expasy.jpl.core.mol.chem.api	Here lies api for chemicals.
org.expasy.jpl.core.mol.chem.impl	Here lies builders and managers for chemicals.
org.expasy.jpl.core.mol.modif	Provides specific kinds of molecular modification objects.
org.expasy.jpl.core.mol.monomer.aa	Provides objects and managers handling amino-acids as molecular symbols and all their biochemical properties like pka or hydropathy measure.
org.expasy.jpl.core.mol.monomer.nuc	Provides objects and managers handling (deoxy)ribonucleotides and symbols.
org.expasy.jpl.core.mol.polymer	Provides bio-polymer objects and tools.
org.expasy.jpl.core.mol.polymer.cutter	Provides objects that cleave polymers like peptidases or restriction enzymes.
org.expasy.jpl.core.mol.polymer.modif	Provides accessors, modificators and managers of molecular modifications for polymers
org.expasy.jpl.core.mol.polymer.modif.unimod
org.expasy.jpl.core.mol.polymer.pept	Provides peptide sequence objects and tools.
org.expasy.jpl.core.mol.polymer.pept.cutter	Provides peptide cutters.
org.expasy.jpl.core.mol.polymer.pept.fragmenter	Provides objects for peptide fragmentation.
org.expasy.jpl.core.mol.polymer.pept.matcher	Provides pattern matcher for peptides.
org.expasy.jpl.core.mol.polymer.pept.rule	Provides editing rules classes for peptides.
org.expasy.jpl.core.mol.polymer.pept.term	Provides peptide terminus objects, types, symbols and managers.
org.expasy.jpl.core.mol.polymer.prot
org.expasy.jpl.core.ms.export	Contains MS data exporters.
org.expasy.jpl.core.ms.lc	Contains liquid chromatography mass spectrometry informations.
org.expasy.jpl.core.ms.spectrum	Provides interfaces and objects for mass spectrometry data.
org.expasy.jpl.core.ms.spectrum.annot	Provides MS fragment annotation objects and manager.
org.expasy.jpl.core.ms.spectrum.annot.comp
org.expasy.jpl.core.ms.spectrum.cons
org.expasy.jpl.core.ms.spectrum.editor	Provides editor objects that modify spectra (adding/removing/modifying peak).
org.expasy.jpl.core.ms.spectrum.editor.intensity	Provides transformers that modify spectra intensities.
org.expasy.jpl.core.ms.spectrum.filter	Provides filters that select peaks in peak list objects.
org.expasy.jpl.core.ms.spectrum.peak	Provides interfaces and objects for peaks in ms peak list.
org.expasy.jpl.core.ms.spectrum.stat	Provides descriptive statistics objects on mass spectrometry data.