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

## Documentation for package ‘biodb’ version 1.4.2

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

## Help Pages

A 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

## -- A --

abstractClass | Declares a class as abstract.
abstractMethod | Declares a method as abstract

## -- B --

biodb | biodb: biodb, a library and a development framework for connecting to chemical and biological databases
BiodbBiocPersistentCache | A persistent cache implementation that uses BiocCache package.
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.
BiodbCustomPersistentCache | A biodb custom persistent cache implementation.
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.
BiodbPersistentCache | The abstract class for handling file caching.
BiodbRequest | Class Request.
BiodbRequestScheduler | Class for handling requests.
BiodbRequestSchedulerRule | Scheduler rule class.
BiodbSdfEntry | 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.
BiodbTxtEntry | Entry class for content in text format.
BiodbUrl | Class URL.
BiodbXmlEntry | Entry class for content in XML format.

## -- C --

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.

## -- D --

df2str | Convert a data.frame into a string.
doesRCurlRequestUrlExist | Test if a URL is valid according to RCurl

## -- 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.
getBaseUrlContent | Get URL content using base::url().
getBaseUrlRequestResult | Get URL request result using base::url().
getConnClassName | Get connector class name.
getConnTypes | Get connector types.
getDefaultCacheDir | Get default cache folder.
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.
getRCurlContent | Get URL content using RCurl::getURL().
getRCurlRequestResult | Get URL request result using RCurcl::getURL().
getReposName | Extract the repository name from a package folder.
getTestOutputDir | Get the test output directory.
getUrlContent | Get a URL content.
getUrlRequestResult | Send a request and get results.

## -- L --

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.

## -- M --

makeRCurlOptions | Build an RCurl::CURLOptions object.
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.

## -- N --

newInst | Create a new BiodbMain instance.

## -- P --

prepareFileContents | Prepares file contents for saving.
Progress | Progress class.

## -- R --

Range | Range class.
RequestResult | Class RequestResult.
runGenericTests | Run generic tests.

## -- S --

saveContentsToFiles | Saves contents to files.
SqliteConn | SQLite connector class.

## -- T --

testContext | Set a test context.
TestRefEntries | A class for accessing the test reference entries.
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.