Package | Description |
---|---|
biolockj |
The root biolockj package contains core classes used by all BioLockJ pipelines.
|
biolockj.module | |
biolockj.module.classifier.r16s |
This package contains RDP and QIIME classifier modules that assign taxonomy to 16s sequences.
Output file formats are classifier specific so classifier requires a unique post-requisite ParserModule . |
biolockj.module.hello_world | |
biolockj.module.report.r |
This package contains
BioModule s that build pipeline reports from the standard OTU abundance
tables by generating R scripts to produce the summary statistics and data visualizations output to PDF files. |
biolockj.node |
Package
biolockj.node contains core classes instantiated by the
ParserModule to hold Sample ID-(OTU name/count) data read in from
ClassifierModule output. |
biolockj.util |
Static utilities centralize and organize reusable core methods.
|
Modifier and Type | Method and Description |
---|---|
static void |
Config.checkDependencies(BioModule module) |
static boolean |
Config.getBoolean(BioModule module,
String property)
Parse property value (Y or N) to return boolean, if not found, return false;
|
static Double |
Config.getDoubleVal(BioModule module,
String property)
Parse property for numeric (double) value
|
static Integer |
Config.getIntegerProp(BioModule module,
String property)
Parse property value as integer
|
static Integer |
Config.getNonNegativeInteger(BioModule module,
String property)
Parse property as non-negative integer value
|
static Double |
Config.getPositiveDoubleVal(BioModule module,
String property)
Parse property as positive double value
|
static Integer |
Config.getPositiveInteger(BioModule module,
String property)
Parse property as positive integer value
|
static boolean |
Config.requireBoolean(BioModule module,
String property)
Required to return a valid boolean or
|
static Double |
Config.requireDoubleVal(BioModule module,
String property)
Requires valid double value
|
static Integer |
Config.requireInteger(BioModule module,
String property)
Requires valid integer value
|
static Double |
Config.requirePositiveDouble(BioModule module,
String property)
Require valid positive double value
|
static Integer |
Config.requirePositiveInteger(BioModule module,
String property)
Require valid positive integer value
|
Modifier and Type | Method and Description |
---|---|
Integer |
ScriptModuleImpl.getTimeout()
Default behavior is for scripts to run indefinitely (no timeout).
|
Integer |
ScriptModule.getTimeout()
ScriptModule that run scripts can opt to set a timeout (such as used by the R script).
|
Modifier and Type | Method and Description |
---|---|
(package private) String |
RdpClassifier.getConfThreshold() |
Modifier and Type | Method and Description |
---|---|
protected String |
Step5.howExciting()
Accesses the "hello.excitmentLevel" and creates a string with that many !s.
|
protected String |
Hello_Friends.howExciting()
Accesses the "hello.excitmentLevel" and creates a string with that many !s, or
just "." if the value is null.
|
protected String |
Step5.makeMessage()
Create a message based on the modules properties.
|
protected String |
Hello_Friends.makeMessage()
Create a message based on the modules properties.
|
Modifier and Type | Method and Description |
---|---|
Integer |
R_Module.getTimeout()
The R Script should run quickly, timeout = 10 minutes appears to work well.
|
Modifier and Type | Method and Description |
---|---|
Map<String,String> |
OtuNodeImpl.getTaxaMap()
This implementation ensures all levels between top and bottom taxonomy levels are complete.
|
protected void |
OtuNodeImpl.populateInBetweenTaxa()
Populate missing OTUs if top level taxa is defined and there is a level gap between the top level and the bottom
level.
|
protected static boolean |
OtuNodeImpl.reportUnclassifiedTaxa() |
Modifier and Type | Method and Description |
---|---|
static void |
BashScriptBuilder.checkDependencies(BioModule module) |
static boolean |
BioLockJUtil.copyInputFiles()
Copy input files into an internal folder within the pipeline root direction named "input"
|
static Integer |
ModuleUtil.getMinSamplesPerWorker(BioModule module)
Return the min number of samples that can be processed per worker script.
|
static Integer |
ModuleUtil.getNumWorkers(BioModule module)
Get the actual number of worker scripts generated for a given module, minimum value = 1.
|
static String |
SeqUtil.getSampleId(File file) |
protected static String |
BashScriptBuilder.getWorkerScriptPath(ScriptModule module)
Build the file path for the numbered worker script.
|
static boolean |
MetaUtil.hasMetaColToSampleIdMap() |
static List<String> |
TaxaUtil.initTaxaLevels()
Set taxonomy levels ordered by level, from highest to lowest.
|
static Boolean |
SeqUtil.isMultiplexed()
Check current state of sequence data.
|
protected static List<String> |
BashScriptBuilder.passEnvironmentVarVals(ScriptModule module) |
static boolean |
MetaUtil.setSampleId(File file,
String sampleId) |
static boolean |
MetaUtil.setSampleId(String filename,
String sampleId) |