Package apollo.config

Interface Summary

ApolloNameAdapterI
DisplayPrefsI
OverlapI	areOverlapping determines if two SeqFeatureIs overlap using the currently defined gene definition (from Config.getGeneDefinition().
PropSchemeChangeListener

Class Summary

ChadoJdbcNameAdapter
ColumnProperty
Config	A class with static data members and static methods for setting and retrieving configuration information for the apollo gui.
DefaultDisplayPrefs
DefaultNameAdapter	If no name adapter is specified, and no or human gene def, then DefaultNameAdapter is used.
EnsjDisplayPrefs
FeatureProperty	FeatureProperty comes from "Types" in the tiers file.
FlyDisplayPrefs
FlyNameAdapter
GmodNameAdapter	This has a lot of stuff that needs to go in FlyNameAdapter subclass.
LinkType	Value class for synteny link types (used by game synteny) if we go to java 1.5 this should be replaced by an enumeration
NoOverlap	as the name implies this overlapper will return false for all areOverlapping queries.
ORF_Overlap	A class detect overlapping transcripts for Drosophila
ParameciumDisplayPrefs
ParameciumNameAdapter
PeptideStatus
PropertyScheme	PropertyScheme is basically the java version of the tiers file.
PropSchemeChangeEvent	Should this be called TierChangeEvent or TypeChangeEvent - it fires for just tiers changing.
RiceNameAdapter
SimpleNameAdapter	This adapter just uses the name of the result to name the annot.
SimpleOverlap	areOverlapping determines if two SeqFeatureIs overlap using the currently defined gene definition (from Config.getGeneDefinition().
Style	A Style is basically config options for a particular data adapter
TierProperty	TierProperty holds a list of FeatureProperties.
TiersIO	Read/write tiers files
TigrAnnotDisplayPrefs	Display preferences for TIGR chado annotation databases.
TigrAnnotNameAdapter	Name adapter for TIGR chado annotation databases.
TigrSybilNameAdapter	TIGR-specific apollo name adapter for Chado.