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validateAlignments.MonteCarloValidation Class Reference
Inheritance diagram for validateAlignments.MonteCarloValidation:
validateAlignments.GenericValidation

Public Member Functions

def __init__
 
def createConfiguration
 
def createScript
 
- Public Member Functions inherited from validateAlignments.GenericValidation
def __init__
 
def createConfiguration
 
def createFiles
 
def createScript
 
def getCompareStrings
 
def getRepMap
 

Additional Inherited Members

- Public Attributes inherited from validateAlignments.GenericValidation
 alignmentToValidate
 
 configFiles
 
 filesToCompare
 
 randomWorkdirPart
 
 scriptFiles
 
- Static Public Attributes inherited from validateAlignments.GenericValidation
string defaultReferenceName = "DEFAULT"
 

Detailed Description

Definition at line 465 of file validateAlignments.py.

Constructor & Destructor Documentation

def validateAlignments.MonteCarloValidation.__init__ (   self,
  alignment,
  config 
)

Definition at line 466 of file validateAlignments.py.

467  def __init__(self, alignment, config):
468  GenericValidation.__init__(self, alignment, config)

Member Function Documentation

def validateAlignments.MonteCarloValidation.createConfiguration (   self,
  path 
)

Definition at line 469 of file validateAlignments.py.

References validateAlignments.GenericValidation.filesToCompare, and validateAlignments.replaceByMap().

470  def createConfiguration(self, path ):
471  cfgName = "TkAlMcValidation.%s_cfg.py"%( self.alignmentToValidate.name )
472  repMap = GenericValidation.getRepMap(self)
473  repMap.update({
474  "APE": configTemplates.APETemplate,
475  "outputFile": replaceByMap( ".oO[workdir]Oo./McValidation_.oO[name]Oo..root", repMap )
476  })
477  repMap["outputFile"] = os.path.expandvars( repMap["outputFile"] )
478  repMap["outputFile"] = os.path.abspath( repMap["outputFile"] )
479  cfgs = {cfgName:replaceByMap( configTemplates.mcValidateTemplate, repMap)}
480  self.filesToCompare[ GenericValidation.defaultReferenceName ] = repMap["outputFile"]
481  GenericValidation.createConfiguration(self, cfgs, path)
def replaceByMap
— Helpers —############################ replaces .oO[id]Oo.
def validateAlignments.MonteCarloValidation.createScript (   self,
  path 
)

Definition at line 482 of file validateAlignments.py.

References validateAlignments.GenericValidation.configFiles, and validateAlignments.replaceByMap().

483  def createScript(self, path):
484  scriptName = "TkAlMcValidate.%s.sh"%( self.alignmentToValidate.name )
485  repMap = GenericValidation.getRepMap(self)
486  repMap["CommandLine"]=""
487  for cfg in self.configFiles:
488  repMap["CommandLine"]+= repMap["CommandLineTemplate"]%{"cfgFile":cfg,
489  "postProcess":""
490  }
491 
492  scripts = {scriptName: replaceByMap( configTemplates.scriptTemplate, repMap ) }
493  return GenericValidation.createScript(self, scripts, path)
def replaceByMap
— Helpers —############################ replaces .oO[id]Oo.