A B C F I M O P R S V

A

appendStrToFile(String, String) - Method in class org.bridgedb.tools.voidtool.VoIDTool

This function adds data to a file without overriding the existing data

B

BridgeQC - Class in org.bridgedb.tools.qc

Utility to do simple quality control on a BridgeDerby database.

BridgeQC(File, File) - Constructor for class org.bridgedb.tools.qc.BridgeQC

Compares two Derby databases and reports the output to STDOUT.

BridgeQC(File, File, OutputStream) - Constructor for class org.bridgedb.tools.qc.BridgeQC

Compares two Derby databases and reports the output to the given OutputStream.

BridgeQC.PropertyChecker - Interface in org.bridgedb.tools.qc

C

check(String, String, PrintStream) - Method in interface org.bridgedb.tools.qc.BridgeQC.PropertyChecker

checkDatabaseSanity() - Method in class org.bridgedb.tools.qc.BridgeQC

compareAttributes() - Method in class org.bridgedb.tools.qc.BridgeQC

compareDataSources() - Method in class org.bridgedb.tools.qc.BridgeQC

compareFileSizes() - Method in class org.bridgedb.tools.qc.BridgeQC

compareInfo() - Method in class org.bridgedb.tools.qc.BridgeQC

compareLinks() - Method in class org.bridgedb.tools.qc.BridgeQC

createRDF() - Method in class org.bridgedb.tools.voidtool.VoIDTool

this method creates RDF file from the derby database passed through the CLI Tool

F

file - Variable in class org.bridgedb.tools.voidtool.VoIDTool

I

initDatabases() - Method in class org.bridgedb.tools.qc.BridgeQC

initDatabases() - Method in class org.bridgedb.tools.voidtool.VoIDTool

M

main(String[]) - Static method in class org.bridgedb.tools.qc.BridgeQC

main(String[]) - Static method in class org.bridgedb.tools.qc.PatternChecker

Script can be run in two ways 1) as part of BridgeQC, to check a single database.

main(String[]) - Static method in class org.bridgedb.tools.voidtool.VoIDTool

O

org.bridgedb.tools.qc - package org.bridgedb.tools.qc

org.bridgedb.tools.voidtool - package org.bridgedb.tools.voidtool

P

PatternChecker - Class in org.bridgedb.tools.qc

Script to check the Id's of one or more derby databases against the patterns registerd in BioDataSources.

PatternChecker() - Constructor for class org.bridgedb.tools.qc.PatternChecker

printUsage() - Static method in class org.bridgedb.tools.qc.BridgeQC

printUsage() - Static method in class org.bridgedb.tools.voidtool.VoIDTool

R

run() - Method in class org.bridgedb.tools.qc.BridgeQC

run(File) - Method in class org.bridgedb.tools.qc.PatternChecker

run() - Method in class org.bridgedb.tools.voidtool.VoIDTool

S

safeEquals(Object, Object) - Static method in class org.bridgedb.tools.qc.BridgeQC

V

VoIDTool - Class in org.bridgedb.tools.voidtool

Utility to extract RDF data from derby database and store it as text file.

VoIDTool(File, String) - Constructor for class org.bridgedb.tools.voidtool.VoIDTool

Reads the database file passed and creates a text file with the name passes containing the RDF data from the database.

A B C F I M O P R S V