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#                                                                         #
# C O P Y R I G H T   N O T I C E                                         #
#  Copyright (c) 2003-10 by:                                              #
#    * California Institute of Technology                                 #
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#
# a simple use of the experiment class
from experiment import Experiment
from analyzeMotifs import AnalyzeMotifs

class VaryLength(Experiment, AnalyzeMotifs):
    experimentType = "varyLength"


    def setRange(self, step, uMin=0, uMax=0, dMin=0, dMax=0):
        self.stepSize      = step
        self.upstreamMin   = uMin
        self.upstreamMax   = uMax + 1
        self.downstreamMin = dMin
        self.downstreamMax = dMax + 1


    def run(self):
        Experiment.run(self)

        for downP in range(self.downstreamMin, self.downstreamMax, self.stepSize):
            for upP in range(self.upstreamMin, self.upstreamMax, self.stepSize):
                self.setSeqParameters(upP, downP)
                # force reloading of the genepool
                self.loadGenepool()
                datasetID = self.genepoolID
                fastaFile = self.createDataFile()
                for (prog, settingsID) in self.programs:
                    prog.inputFile(fastaFile)
                    # reset setttings to orig settings, set new length, save settings
                    prog.setSettings(self.settings[settingsID])
                    prog.setSeqLength(str(upP + downP))
                    newestSettingsID = self.setSettings(prog.getSettings())
                    runID = self.setRun(prog.name(), datasetID, newestSettingsID)
                    tag = str(runID)
                    prog.setTagID(tag)
                    prog.run()
                    theMotifs = prog.getMotifs()
                    for mot in theMotifs:
                        self.results.append(mot)