Man pages for pkrog/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 |
| BiodbBiocPersistentCache | A persistent cache implementation that uses BiocCache... |
| 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... |
| 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. |
| biodb-package | biodb: biodb, a library and a development framework for... |
| 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. |
| 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. |
| doesRCurlRequestUrlExist | Test if a URL is valid according to RCurl |
| 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 |
| FileTemplate | File template class. |
| 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. |
| 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. |
| 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... |
| MassSqliteEntry | Mass spectra SQLite entry class. |
| newInst | Create a new BiodbMain instance. |
| prepareFileContents | Prepares file contents for saving. |
| Progress | Progress class. |
| Range | Range class. |
| RequestResult | Class RequestResult. |
| runGenericTests | Run generic tests. |
| saveContentsToFiles | Saves contents to files. |
| SqliteConn | SQLite connector class. |
| testContext | Set a test context. |
| TestRefEntries | A class for accessing the test reference entries. |
| testThat | Run a test. |
| upgradeExtPkg | Upgrading an existing extension package for biodb. |
| warn | Throw a warning and log it too. |
| warn0 | Throw a warning and log it too. |
