Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases

---

Documentation for package ‘biodb’ version 1.16.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

biodb-package	biodb: Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases
abstractClass	Declares a class as abstract.
abstractMethod	Declares a method as abstract
biodb	biodb: Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases
BiodbConfig	A class for storing configuration values.
BiodbConn	The mother abstract class of all database connectors.
BiodbConnBase	Base class of 'BiodbConn' for encapsulating all needed information for database access.
BiodbCsvEntry	Entry class for content in CSV format.
BiodbDbInfo	A class for describing the characteristics of a database.
BiodbDbsInfo	A class for describing the available databases.
BiodbEntry	The mother abstract class of all database entry classes.
BiodbEntryField	A class for describing an entry field.
BiodbEntryFields	A class for handling description of all entry fields.
BiodbFactory	A class for constructing biodb objects.
BiodbHtmlEntry	Entry class for content in HTML format.
BiodbJsonEntry	Entry class for content in JSON format.
BiodbListEntry	Entry class for content in list format.
BiodbMain	The central class of the biodb package.
BiodbSdfEntry	Entry class for content in SDF format.
BiodbTestMsgAck	A class for acknowledging messages during tests.
BiodbTxtEntry	Entry class for content in text format.
BiodbXmlEntry	Entry class for content in XML format.
checkDeprecatedCacheFolders	Check deprecated default cache folders.
closeMatchPpm	Close match PPM
CompCsvFileConn	Compound CSV File connector class.
CompCsvFileEntry	Compound CSV File entry class.
CompSqliteConn	Class for handling a Compound database in SQLite format.
CompSqliteEntry	Compound SQLite entry class.
connNameToClassPrefix	Convert connector name into class prefix.
createBiodbTestInstance	Creating a BiodbMain instance for tests.
CsvFileConn	CSV File connector class.
df2str	Convert a data.frame into a string.
error	Throw an error and log it too.
error0	Throw an error and log it too.
FileTemplate	File template class.
getConnClassName	Get connector class name.
getConnTypes	Get connector types.
getDefaultCacheDir	Get default cache folder.
getEntryClassName	Get entry class name.
getEntryTypes	Get entry types.
getLogger	Get the main package logger.
listTestRefEntries	List test reference entries.
loadFileContents	Loads the contents of files in memory.
logDebug	Log debug message.
logDebug0	Log debug message.
logInfo	Log information message.
logInfo0	Log information message.
logTrace	Log trace message.
logTrace0	Log trace message.
lst2str	Convert a list into a string.
MassCsvFileConn	Mass CSV File connector class.
MassCsvFileEntry	Mass CSV File entry class.
MassSqliteConn	Class for handling a Mass spectrometry database in SQLite format.
MassSqliteEntry	Mass spectra SQLite entry class.
newInst	Create a new BiodbMain instance.
Progress	Progress class.
Range	Range class.
runGenericTests	Run generic tests.
SqliteConn	SQLite connector class.
testContext	Set a test context.
TestRefEntries	A class for accessing the test reference entries.
testThat	Run a test.
warn	Throw a warning and log it too.
warn0	Throw a warning and log it too.