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AASequence.BioPolymer
concatenation (modifications handled).Weighable mass calculators will have to extend this class and
implement computeMonoAndAvgMasses(T o).Symbol to its
Molecule by coupling a table of molecular symbols with the molecular
pool.Annotatable may have 0 to many ms fragments
annotations FragmentAnnotations by position.BinnedPeakList interface should be implemented by any compressed
peaklist objects composed of bins or intervals of mzs.BinnedPeakList is a "compressed" ms peak list where each bin is an
interval of mzs defined by a bin width.binNumber bins, the bins precision
is deduced.Polymer is a macromolecule composed of repeating structural units
represented by Molecule and symbolised by Symbol typically
connected by covalent chemical bonds.BioPolymerModifContainer is a container that stores
modifications by index.ModifParser that can parse a
string to find localized modifications and keep the non-modified sequence
needed for instanciation from SymbolSequence.Builder.BioPolymers.BinnedPeakListImpl.
JPLModifManager.
JPLModifManager.
ChemicalFacade is the only entry point to fetch atoms or molecules.this instance.
MotifMatchers of cutting site in
polymers.Digester handles the digestion of amino-acid sequences by Peptidase.BioPolymer edition (amino-acid
modification).Element is composed of Isotopes.ElementManager is a central entry point for access to all atoms and
isotopes.FragmentAnnotation interface should be implemented by any class that
define fragment annotation type instance.FragmentAnnotation by priority level given
internal class FragmentRuleMatcher knowing a set of conditions on
annotation dods and the given annotation.FragmentAnnotation.FragmentAnnotations on Annotatable
objects.Fragmenter interface should be implemented by any fragmenters
handling the theoretical fragmentation of AASequences.distId.
peptide1 - peptide2.
distId.
IonizableGroup from mandatory and
optional parameters.IonizableModification is a Modification containing one or
many ionizable molecular entities.IonizableMolecule is a Molecule containing one or many
ionizable molecular entities.Isotope is a simple implementation of Atom.MassCalculator computes mass of any chemicals.ModifContainer is a simple modifications' container.String format for Modification.Modification with multiple static
factory methods for instanciation.Molecule with a Modification.Molecule.MSPeakListDistributions into files and generate R
scripts for rendering.EditionRule with alternative actions.
Molecule.
PeakChecker provides utilities to test peaks'validity.PeakList interface should be implemented by any mass spectrum
object that stores peaks with masses-to-charge-ratio, intensities and
annotations.PeakListImpl.PeakLists.PeakLists.Peptidase is defined by a name and a cleavage site that match the
sites to be digested.Peptidases.Peptide is a BioPolymer of amino-acid residues with N/C
terminals represented as the monomeric formula NH-CHRn-CO (AAs).Peptides from one instance given specific
edition rules.PeptideFragmenter fails to fragment a peptide.PeptideFragmentProcessor interface should be implemented by any
builder building T type instance.Peptide precursor and a
FragmentationConfig or a FragmentAnnotation.Peptide.Peptides.Peptide in the context of a list of amino-acids.PeptideTypes.Condition on a PeptideType.TerminusTypes.BioPolymer have to extends this interface.Molecule NTerminus and CTerminus).Modifications in the pool handled by ModifManager from the file 'unimod.xml'.Molecule
JPLNeutralLoss from a Modification.
Peptide from a list of molecules.
FragmentAnnotationImpl if already cached.
Weighable interface should be implemented by any object that has
a molecular mass measured at specific accuracy.JPLNeutralLoss from a Modification.
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