Uses of Class
biolockj.Properties

Packages that use Properties

Package	Description
biolockj	The root biolockj package contains core classes used by all BioLockJ pipelines.

Uses of Properties in biolockj

Methods in biolockj that return Properties

Modifier and Type	Method and Description
protected static Properties	Properties.buildConfig(File propFile) Recursive method handles nested default Config files.
static Properties	Properties.loadProperties(File file) Instantiate Properties via buildConfig(File)
protected static Properties	Properties.readProps(File propFile, Properties defaultProps) Read the properties defined in the required propFile and defaultProps (if included) to build Config. Properties in propFile will override the defaultProps.
protected static Properties	Config.replaceEnvVars(Properties properties) Interpret env variables defined in the Config file and runtime env - for example These props are used in: $BLJ/resources/config/defult/docker.properties: BLJ_ROOT=/mnt/efs EFS_DB=${BLJ_ROOT}/db humann2.protDB=${EFS_DB}/uniref Therefore, getString( "humann2.protDB" ) returns "/mnt/efs/db/uniref" If not found, check runtiem env (i.e., $HOME/bash_profile)

Methods in biolockj with parameters of type Properties

Modifier and Type	Method and Description
protected static Properties	Properties.readProps(File propFile, Properties defaultProps) Read the properties defined in the required propFile and defaultProps (if included) to build Config. Properties in propFile will override the defaultProps.
protected static Properties	Config.replaceEnvVars(Properties properties) Interpret env variables defined in the Config file and runtime env - for example These props are used in: $BLJ/resources/config/defult/docker.properties: BLJ_ROOT=/mnt/efs EFS_DB=${BLJ_ROOT}/db humann2.protDB=${EFS_DB}/uniref Therefore, getString( "humann2.protDB" ) returns "/mnt/efs/db/uniref" If not found, check runtiem env (i.e., $HOME/bash_profile)

Constructors in biolockj with parameters of type Properties

Constructor and Description
Properties(Properties defaultConfig) Constructor called when "pipeline.defaultProps" contains a valid file-path