de.hu.berlin.wbi.objects (SETH documentation)

Class Summary
Class	Description
AminoAcidHelper	Helper class to transform a one letter amino-acid into a three letter representation
DatabaseConnection	Convenience class for database communication
dbSNP	Represents a dbSNP entry; loaded from a local database.
dbSNPNormalized	Represents a `MutationMention` mention which has been successfully normalized to a `dbSNP` .
EntityOffset	Represents the text span of entity mentions (`MutationMention`, `Gene`, etc.).
Gene	Represents a gene mention found by any Named Enttiy Recognition and Normalization tool.
HGVS	Represents a HGVS reference, like `NR_027062.1:c.157+25766C>T`.
MutationMention	Class to represent a mutation mention found by an NER tool like MutationFinder or SETH
MutationValidation	This object represents a `MutationMention` from the validation corpus, where we already know which `dbSNP` entry is associated with this gene.
Transcript	Class to represents a transcript (Protein as well as coding sequence) Therefore one gene usually contains one or more `Transcript`
TranscriptNormalized	Represents a `MutationMention` mention which has been successfully normalized to a `Transcript` .
UniprotFeature	Represents a UniProt entry; loaded from database.

Enum Summary
Enum	Description
MatchOptions	Represents the different possibilities to match a `MutationMention` to a dbSNP entry or UniProt entry
MutationMention.Tool	Enumeration of all named entity recognition components

Package de.hu.berlin.wbi.objects Description

Package with the main data objects.