savant.ucsc

Class UCSCDataSourcePlugin

java.lang.Object

savant.plugin.SavantPlugin

savant.plugin.SavantDataSourcePlugin

savant.sql.SQLDataSourcePlugin

savant.ucsc.UCSCDataSourcePlugin

All Implemented Interfaces:

savant.sql.SQLConstants

public class UCSCDataSourcePlugin
extends savant.sql.SQLDataSourcePlugin
implements savant.sql.SQLConstants

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

Author:

tarkvara

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	STANDARD_CLADES

Fields inherited from class savant.sql.SQLDataSourcePlugin

DOWNLOAD_URL_SETTING, DRIVER_NAME_SETTING, driverName, LOG, password, PASSWORD_SETTING, uri, URI_SETTING, USER_SETTING, userName

Fields inherited from interface savant.sql.SQLConstants

BLOCK_ENDS, BLOCK_SIZES, BLOCK_STARTS_ABSOLUTE, BLOCK_STARTS_RELATIVE, CHROM, COUNT, DATA_RANGE, END, FILE, ITEM_RGB, LOWER_LIMIT, NAME, NAME2, NO_COLUMN, OFFSET, SCORE, SPAN, START, STRAND, THICK_END, THICK_START, VALUE

Constructor Summary

Constructors

Constructor and Description
UCSCDataSourcePlugin()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	canOpen(URI uri)
String	findCladeForGenome(GenomeDef g) Figure out which clade contains the given genome.
savant.sql.Table	findTable(String track) Look through the database's tables for one representing this track.
GenomeDef[]	getCladeGenomes(String clade) Get all the genomes which are available for the given clade.
GenomeDef	getCurrentGenome(String clade)
List<String>	getReferences(savant.sql.MappedTable table) Get a list of references for this data-source.
savant.sql.MappedTable	getTableByName(String tableName, String dbName, String trackName) Get a table with the columns mapped based on saved settings.
savant.sql.MappedTable	getTableWithStandardMapping(TrackDef t) Get a set of mappings for a track which has not been configured using the navigation dialog.
String	getTitle()
void	init()
protected savant.sql.MappedTable	requestMapping(savant.sql.Table t) 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.
void	selectGenomeDB(savant.sql.Table t) Select the current genome database based on the given table.
protected void	tryToLogin(boolean silent) Logging into UCSC is always done silently, without a login dialog.

Methods inherited from class savant.sql.SQLDataSourcePlugin

getConnection, getDatabase, getDatabases, getDataSource, getDataSource, saveSettings

Methods inherited from class savant.plugin.SavantPlugin

getDescriptor, setDescriptor, shutDown

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

STANDARD_CLADES

public static final String[] STANDARD_CLADES

Constructor Detail

UCSCDataSourcePlugin

public UCSCDataSourcePlugin()

Method Detail

init

public void init()

Overrides:

init in class savant.sql.SQLDataSourcePlugin

canOpen

public boolean canOpen(URI uri)

Overrides:

canOpen in class savant.sql.SQLDataSourcePlugin

tryToLogin

protected void tryToLogin(boolean silent)
                   throws ClassNotFoundException,
                          SQLException

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

Overrides:

tryToLogin in class savant.sql.SQLDataSourcePlugin

Parameters:

silent - ignored

Throws:

ClassNotFoundException

SQLException

requestMapping

protected savant.sql.MappedTable requestMapping(savant.sql.Table t)
                                         throws SQLException

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.

Overrides:

requestMapping in class savant.sql.SQLDataSourcePlugin

Throws:

SQLException

getTitle

public String getTitle()

Overrides:

getTitle in class savant.sql.SQLDataSourcePlugin

getReferences

public List<String> getReferences(savant.sql.MappedTable table)
                           throws SQLException

Get a list of references for this data-source. If there is a mapping for the chrom field, use that. If not, use the chromInfo table to determine the list of chromosomes for this genome. This is necessary to support certain UCSC tracks where the data is spread over one chromosome per table.

Overrides:

getReferences in class savant.sql.SQLDataSourcePlugin

Throws:

SQLException

getTableByName

public savant.sql.MappedTable getTableByName(String tableName,
                                    String dbName,
                                    String trackName)
                                      throws SQLException

Get a table with the columns mapped based on saved settings. In theory, the mappings will have been saved during some earlier visit to the UCSC Navigation Dialog.

Overrides:

getTableByName in class savant.sql.SQLDataSourcePlugin

Throws:

SQLException

findTable

public savant.sql.Table findTable(String track)
                           throws SQLException

Look through the database's tables for one representing this track. It can be: 1) an exact match for the track name 2) equal to "all_" plus the track name 3) equal to the chromosome name plus the track name (e.g. "chr1_rmsk" and friends) Intererstingly enough, since the initial development of this plugin, UCSC seems to have replaced all occurrences of case 3) with case 2). Nonetheless, the code for case 3) remains here just in case UCSC missed a few tracks.

Throws:

SQLException

getTableWithStandardMapping

public savant.sql.MappedTable getTableWithStandardMapping(TrackDef t)

Get a set of mappings for a track which has not been configured using the navigation dialog. This is used by the UCSC chooser dialog to avoid the mapping dialog as much as possible.

Parameters:

t - the track for which we're getting the mapping

Returns:

a table with associated (possibly null) column mappings

getCladeGenomes

public GenomeDef[] getCladeGenomes(String clade)

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

Parameters:

clade - one of the six standard clades

Returns:

findCladeForGenome

public String findCladeForGenome(GenomeDef g)

Figure out which clade contains the given genome.

Parameters:

g -

Returns:

getCurrentGenome

public GenomeDef getCurrentGenome(String clade)

selectGenomeDB

public void selectGenomeDB(savant.sql.Table t)

Select the current genome database based on the given table. If the table is null, use the current genome. If the genome is null, look for "GENOME" in the settings. If that is null, use "hg18".

Parameters:

t -