biodb, a library and a development framework for connecting to chemical and biological databases

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Documentation for package ‘biodb’ version 1.0.0

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B C D E F G L M N P R S T U W

biodb-package biodb: biodb, a library and a development framework for connecting to chemical and biological databases

-- B --

biodb biodb: biodb, a library and a development framework for connecting to chemical and biological databases
BiodbCompounddbConn An interface for all compound databases.
BiodbCompounddbConn-class An interface for all compound databases.
BiodbConfig A class for storing configuration values.
BiodbConfig-class A class for storing configuration values.
BiodbConn The mother abstract class of all database connectors.
BiodbConn-class The mother abstract class of all database connectors.
BiodbConnBase Base class of 'BiodbConn' for encapsulating all needed information for database access.
BiodbConnBase-class Base class of 'BiodbConn' for encapsulating all needed information for database access.
BiodbConnObserver The observer class of connectors.
BiodbConnObserver-class The observer class of connectors.
BiodbCsvEntry Entry class for content in CSV format.
BiodbCsvEntry-class Entry class for content in CSV format.
BiodbDbInfo A class for describing the characteristics of a database.
BiodbDbInfo-class A class for describing the characteristics of a database.
BiodbDbsInfo A class for describing the available databases.
BiodbDbsInfo-class A class for describing the available databases.
BiodbDownloadable An abstract class (more like an interface) to model a remote database that can be downloaded locally.
BiodbDownloadable-class An abstract class (more like an interface) to model a remote database that can be downloaded locally.
BiodbEditable An interface to model an editable database.
BiodbEditable-class An interface to model an editable database.
BiodbEntry The mother abstract class of all database entry classes.
BiodbEntry-class The mother abstract class of all database entry classes.
BiodbEntryField A class for describing an entry field.
BiodbEntryField-class A class for describing an entry field.
BiodbEntryFields A class for handling description of all entry fields.
BiodbEntryFields-class A class for handling description of all entry fields.
BiodbFactory A class for constructing biodb objects.
BiodbFactory-class A class for constructing biodb objects.
BiodbHtmlEntry Entry class for content in HTML format.
BiodbHtmlEntry-class Entry class for content in HTML format.
BiodbJsonEntry Entry class for content in JSON format.
BiodbJsonEntry-class Entry class for content in JSON format.
BiodbListEntry Entry class for content in list format.
BiodbListEntry-class Entry class for content in list format.
BiodbMain The central class of the biodb package.
BiodbMain-class The central class of the biodb package.
BiodbMassdbConn The mother class of all Mass spectra databases.
BiodbMassdbConn-class The mother class of all Mass spectra databases.
BiodbObserver The mother abstract class of all observer classes.
BiodbObserver-class The mother abstract class of all observer classes.
BiodbPersistentCache A class for handling file caching.
BiodbPersistentCache-class A class for handling file caching.
BiodbRemotedbConn The mother class of all remote database connectors.
BiodbRemotedbConn-class The mother class of all remote database connectors.
BiodbRequest Class Request.
BiodbRequestScheduler Class for handling requests.
BiodbRequestScheduler-class Class for handling requests.
BiodbRequestSchedulerRule Scheduler rule class.
BiodbSdfEntry Entry class for content in SDF format.
BiodbSdfEntry-class Entry class for content in SDF format.
BiodbSqlBinaryOp This class represents an SQL binary operator.
BiodbSqlExpr The SQL Expression abstact class.
BiodbSqlField This class represents an SQL field.
BiodbSqlList This class represents an SQL list.
BiodbSqlLogicalOp This class represents an SQL logical operator.
BiodbSqlQuery This class handles an SQL Query.
BiodbSqlValue This class represents an SQL value.
BiodbTestMsgAck A class for acknowledging messages during tests.
BiodbTestMsgAck-class A class for acknowledging messages during tests.
BiodbTxtEntry Entry class for content in text format.
BiodbTxtEntry-class Entry class for content in text format.
BiodbUrl Class URL.
BiodbWritable An abstract class (more like an interface) to model a writable database.
BiodbWritable-class An abstract class (more like an interface) to model a writable database.
BiodbXmlEntry Entry class for content in XML format.
BiodbXmlEntry-class Entry class for content in XML format.

-- C --

closeMatchPpm Close match PPM
CompCsvFileConn Compound CSV File connector class.
CompCsvFileConn-class Compound CSV File connector class.
CompCsvFileEntry Compound CSV File entry class.
CompCsvFileEntry-class Compound CSV File entry class.
CompSqliteConn Class for handling a Compound database in SQLite format.
CompSqliteConn-class Class for handling a Compound database in SQLite format.
CompSqliteEntry Compound SQLite entry class.
CompSqliteEntry-class Compound SQLite entry class.
connNameToClassPrefix Convert connector name into class prefix.
createBiodbTestInstance Creating a BiodbMain instance for tests.
CsvFileConn CSV File connector class.
CsvFileConn-class CSV File connector class.

-- D --

df2str Convert a data.frame into a string.

-- E --

error Throw an error and log it too.
error0 Throw an error and log it too.
ExtConnClass Extension connector clas
ExtCpp Extension C++ code class
ExtDefinitions Extension defintions file class
ExtDescriptionFile Extension DESCRIPTION file
ExtEntryClass Extension entry class
ExtFileGenerator Extension file generator abstract class
ExtGenerator Extension generator abstract class
ExtGitignore Extension Gitignore file class
ExtLicense Extension license
ExtMakefile Extension Makefile
ExtPackage Extension package class
ExtPackageFile Extension package file class.
ExtRbuildignore Extension Rbuildignore file class
ExtReadme Extension README file class
ExtTests Extension tests class
ExtTravisFile Extension Travis YAML file generator class
ExtVignette Extension vignette class

-- F --

FileTemplate File template class.

-- G --

genNewExtPkg Generate a new extension package for biodb.
getConnClassName Get connector class name.
getConnTypes Get connector types.
getEntryClassName Get entry class name.
getEntryTypes Get entry types.
getLicenses Get the available licenses for extension packages.
getLogger Get the main package logger.
getPkgName Get the package name from a package folder path.
getReposName Extract the repository name from a package folder.
getTestOutputDir Get the test output directory.

-- L --

listTestRefEntries List test reference entries.
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.

-- M --

MassCsvFileConn Mass CSV File connector class.
MassCsvFileConn-class Mass CSV File connector class.
MassCsvFileEntry Mass CSV File entry class.
MassCsvFileEntry-class Mass CSV File entry class.
MassSqliteConn Class for handling a Mass spectrometry database in SQLite format.
MassSqliteConn-class Class for handling a Mass spectrometry database in SQLite format.
MassSqliteEntry Mass spectra SQLite entry class.
MassSqliteEntry-class Mass spectra SQLite entry class.

-- N --

newInst Create a new BiodbMain instance.

-- P --

Progress Progress class.

-- R --

Range Range class.
runGenericTests Run generic tests.

-- S --

SqliteConn SQLite connector class.
SqliteConn-class SQLite connector class.

-- T --

testContext Set a test context.
testThat Run a test.

-- U --

upgradeExtPkg Upgrading an existing extension package for biodb.

-- W --

warn Throw a warning and log it too.
warn0 Throw a warning and log it too.