C D E F G H I R S T U

C

canOpen(URI) - Method in class savant.ucsc.UCSCDataSourcePlugin

CladesFetcher - Class in savant.ucsc

Worker which fetches information about the clades available in the UCSC database.

CladesFetcher(UCSCDataSourcePlugin) - Constructor for class savant.ucsc.CladesFetcher

D

doInBackground() - Method in class savant.ucsc.CladesFetcher

doInBackground() - Method in class savant.ucsc.GroupsFetcher

E

equals(Object) - Method in class savant.ucsc.GenomeDef

equals(Object) - Method in class savant.ucsc.TrackDef

F

findCladeForGenome(GenomeDef) - Method in class savant.ucsc.UCSCDataSourcePlugin

Figure out which clade contains the given genome.

findTable(String) - Method in class savant.ucsc.UCSCDataSourcePlugin

Look through the database's tables for one representing this track.

G

GenomeDef - Class in savant.ucsc

Class which keeps track of information about a genome in the UCSC database, most importantly the name of the associated MySQL database.

GenomeDef(String, String) - Constructor for class savant.ucsc.GenomeDef

getCladeGenomes(String) - Method in class savant.ucsc.UCSCDataSourcePlugin

Get all the genomes which are available for the given clade.

getCurrentGenome(String) - Method in class savant.ucsc.UCSCDataSourcePlugin

getDatabase() - Method in class savant.ucsc.GenomeDef

getMapping() - Method in class savant.ucsc.UCSCNavigationDialog

getReferences(MappedTable) - Method in class savant.ucsc.UCSCDataSourcePlugin

Get a list of references for this data-source.

getTableByName(String, String, String) - Method in class savant.ucsc.UCSCDataSourcePlugin

Get a table with the columns mapped based on saved settings.

getTableName() - Method in class savant.ucsc.TrackDef

getTableWithStandardMapping(TrackDef) - Method in class savant.ucsc.UCSCDataSourcePlugin

Get a set of mappings for a track which has not been configured using the navigation dialog.

getTitle() - Method in class savant.ucsc.UCSCDataSourcePlugin

getTrackName() - Method in class savant.ucsc.TrackDef

getTracks() - Method in class savant.ucsc.GroupDef

GroupDef - Class in savant.ucsc

Class which keeps track of information about a given track grouping in the UCSC database.

GroupsFetcher - Class in savant.ucsc

SQL worker which is responsible for fetching the track groups for a given genome.

GroupsFetcher(UCSCDataSourcePlugin, GenomeDef) - Constructor for class savant.ucsc.GroupsFetcher

H

hashCode() - Method in class savant.ucsc.GenomeDef

hashCode() - Method in class savant.ucsc.TrackDef

I

init() - Method in class savant.ucsc.UCSCDataSourcePlugin

R

requestMapping(Table) - Method in class savant.ucsc.UCSCDataSourcePlugin

Instead of showing the base-class MappingDialog, the UCSC plugin builds up the list of tables from the hgcentral database and displays a UCSC-specific dialog.

S

savant.ucsc - package savant.ucsc

selectGenomeDB(Table) - Method in class savant.ucsc.UCSCDataSourcePlugin

Select the current genome database based on the given table.

STANDARD_CLADES - Static variable in class savant.ucsc.UCSCDataSourcePlugin

T

toString() - Method in class savant.ucsc.GenomeDef

toString() - Method in class savant.ucsc.GroupDef

toString() - Method in class savant.ucsc.TrackDef

TrackDef - Class in savant.ucsc

Class which keeps track of information about a single track within the UCSC database.

tryToLogin(boolean) - Method in class savant.ucsc.UCSCDataSourcePlugin

Logging into UCSC is always done silently, without a login dialog.

U

UCSCDataSourcePlugin - Class in savant.ucsc

A version of the SQL data-source plugin which is configured to work nicely with the UCSC database.

UCSCDataSourcePlugin() - Constructor for class savant.ucsc.UCSCDataSourcePlugin

UCSCNavigationDialog - Class in savant.ucsc

UCSC-specific dialog for selecting the desired table.

UCSCNavigationDialog(Window, UCSCDataSourcePlugin, Table) - Constructor for class savant.ucsc.UCSCNavigationDialog

Dialog which lets the user navigate through the UCSC hierarchy and select the table they want.

C D E F G H I R S T U