MGT::Proj::SynecApp::SynecApp Class Reference

Inheritance diagram for MGT::Proj::SynecApp::SynecApp:

List of all members.

Public Member Functions
def	parseCmdLinePost
def	doWork
def	makeSeqRecIdLabs
Static Public Attributes
tuple	batchDepModes = ("parscan",)
	Derived classes should set this to a list of opt.mode values that can result in submision of new batch jobs.

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Detailed Description

App-derived class for synecoccus classification

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Member Function Documentation

def MGT::Proj::SynecApp::SynecApp::doWork	(		self,
			kw
	)

Do the actual work.
Must be redefined in the derived classes.
Should not be called directly by the user except from doWork() in a derived class.
Should work with empty keyword dict, using only self.opt.
If doing batch submision of other App instances, must return a list of sink (final) BatchJob objects.

Reimplemented from MGT::App::App.

def MGT::Proj::SynecApp::SynecApp::makeSeqRecIdLabs

(

self )

Build IdLabels object from seqRec descriptions

def MGT::Proj::SynecApp::SynecApp::parseCmdLinePost	(		klass,
			options,
			args,
			parser
	)

Optionally modify options and args in-place.
Called at the end of parseCmdLine to allow the derived classes customizing the option processing.
@param options options returned by OptionParser and converted to Struct object
@param args args returned by OptionParser
@param parser OptionParser object used to parse the command line - needed here to call its error() method
if necessary.
options should be modified in place by this method

Reimplemented from MGT::App::App.

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Member Data Documentation

tuple MGT::Proj::SynecApp::SynecApp::batchDepModes = ("parscan",) [static]

Derived classes should set this to a list of opt.mode values that can result in submision of new batch jobs.

Reimplemented from MGT::App::App.

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The documentation for this class was generated from the following file:

• mgtaxa/MGT/Proj/SynecApp.py