caferror.py File Reference

Namespaces
	caferror

Functions
def	caferror.errorOut
	Function Definitions. More...
def	caferror.optParse
def	caferror.printWrite
def	caferror.cafeRun
def	caferror.errFileCheck
def	caferror.getScore
def	caferror.maxfamsize

Variables
tuple	caferror.startsec = time.time()
	Main Block. More...
tuple	caferror.start = datetime.datetime.now()
string	caferror.initCheck = ""
list	caferror.spec_to_min = []
int	caferror.rmlog = 0
int	caferror.FilterFlag = 0
tuple	caferror.inFile = open(inFilename, "r")
tuple	caferror.inLines = inFile.readlines()
list	caferror.CafePath = inLines[x]
list	caferror.FamFile = inLines[x]
list	caferror.Tree = inLines[x]
list	caferror.LamStruct = inLines[x]
list	caferror.t_struct = LamStruct[LamStruct.index("-t"):]
list	caferror.treestring = Tree[Tree.index("("):]
	caferror.caferrorLog = tmpDir+caferrorLog;
tuple	caferror.clogfile = open(caferrorLog, "w")
	caferror.outFilename = tmpDir+outFilename;
tuple	caferror.outFile = open(outFilename, "w")
int	caferror.pad = 35
	Begin input info block! More...
int	caferror.numruns = 1
	End input info block! More...
	caferror.preScore = lastScore;
	caferror.preLam = lastLam;
list	caferror.errList = []
	Global error estimation begins here for -c 0 (default) More...
	caferror.errMin = initError;
	caferror.minScore = lastScore;
	Global error estimation begins here for -c 1. More...
	caferror.lastError = initError;
float	caferror.nextError = 0.0
	The main logic statements of the code are below. More...
float	caferror.posLimit = 1.0
	caferror.posLimScore = lastScore;
float	caferror.negLimit = 0.0
float	caferror.negLimScore = 0.0
int	caferror.currentError = initError/2
	if Mode == 1 or Mode == 3: overallMinScore = currentScore; Toggle this line to either keep the background constant (commented) or update it each time a species is minimized. More...
int	caferror.tally = 0
int	caferror.keepGoing = 1
	These are the termination scenarios. More...
	caferror.megLimScore = lastScore;
	caferror.minLam = currentLam;
	caferror.lastScore = currentScore;
dictionary	caferror.finalSpecDict = {}
	Individual species error estimation begins here if -s 1. More...
	caferror.overallMinScore = minScore;
list	caferror.moreErrSpec = []
	caferror.specMinScore = minScore;
	caferror.oldspecMin = minScore;
int	caferror.zcheck = 0
int	caferror.minimized = 0
	caferror.specMinErr = errMin;
	if Mode == 1 or Mode == 3: More...
string	caferror.check = "higher than"
string	caferror.check2 = "will not be further minimized."
tuple	caferror.numrnuns = cafeRun(FamFile, Tree, LamStruct, CafePath, tmpDir, caferrorLog, finalSpecDict, spec_to_min, rmlog, FilterFlag, numruns, vOpt)
	The final CAFE run which generates a report with the minimized error. More...
tuple	caferror.endsec = time.time()
	Main output block. More...
tuple	caferror.runtime = (float(endsec) - float(startsec))
tuple	caferror.end = datetime.datetime.now()