Constant Class Reference

#include <types.hh>

Static Public Member Functions
static void	init ()
static string	fullSpeciesPath ()
static string	modelPath ()
static string	extrinsicPath ()
static int	ass_size ()
static int	ass_whole_size ()
static int	dss_size ()
static int	dss_whole_size ()

Static Public Attributes
static string	configPath
static string	speciesDir
static int	decomp_num_at = 1
static int	decomp_num_gc = 1
static int	decomp_num_steps = 1
static int	trans_init_window = 12
static int	tis_maxbinsize = 0
static int	ass_upwindow_size = 20
static int	init_coding_len = 16
static int	et_coding_len = 5
static int	ass_start = 2
static int	ass_end = 2
static int	dss_start = 2
static int	dss_end = 5
static int	dss_maxbinsize = 0
static int	ass_maxbinsize = 0
static int	tss_upwindow_size = 0
static int	tss_start = 5
static int	min_coding_len = 102
static int	max_exon_len = 12000
static Integer	d_polyasig_cleavage = 20
static bool	keep_viterbi = false
static double	gc_range_min = 0.32
static double	gc_range_max = 0.73
static double	probNinCoding = 0.23
static double	opalprob = 0.333
static double	amberprob = 0.333
static double	ochreprob = 0.333
static bool	utr_option_on = false
static bool	nc_option_on = false
static Integer	augustus_verbosity = 1
static bool	alternatives_from_evidence = true
static double	subopt_transcript_threshold = 0.94
static Integer	almost_identical_maxdiff = 10
static bool	uniqueGeneId = false
static double	max_contra_supp_ratio = 9.0
static bool	reportUtrOnlyGenes = false
static bool	useCRFtraining = false
static bool	CRFtrainTIS = true
static bool	CRFtrainSS = true
static bool	CRFtrainIntron = true
static bool	CRFtrainIgenic = true
static bool	CRFtrainCDS = true
static bool	CRFtrainUTR = false
static bool	dss_gc_allowed = false
static Boolean	tieIgenicIntron = true
static Boolean	exoncands = false
static Boolean	proteinOutput = true
static Boolean	codSeqOutput = false
static Boolean	contentmodels = true
static Integer	min_intron_len = 39
static bool	MultSpeciesMode = 0
static string	treefile
static string	speciesfilenames
static string	dbaccess
static string	alnfile
static string	codonalnfile
static bool	overlapmode = false
static Boolean	printEvidence = true
static Boolean	printExonCandsMSA = false
static Boolean	printOEs = false
static Boolean	printHints = false
static Boolean	printMEA = false
static Boolean	printSampled = false
static Boolean	printGeneRangesBED = false
static Boolean	printGeneRangesGFF = false
static Integer	maxOvlp = 60
static vector< Double >	head2tail_ovlp
static vector< Double >	head2head_ovlp
static vector< Double >	tail2tail_ovlp
static unsigned	temperature = 0
static bool	softmasking = true
static bool	softmasking_explicitly_requested = false
static bool	dbhints = false
static bool	logreg
static string	referenceFile
static string	refSpecies
static double	GD_stepsize = 0.01
static bool	rLogReg = false
static double	label_flip_prob = 0.01
static double	lambda = 0
static vector< double >	ex_sc
static vector< double >	in_sc
static int	oeExtensionWidth
static vector< double >	lg_es
static bool	computeNumSubs
static bool	useAArates
static bool	useNonCodingModel
static bool	rescaleBoni = true

Detailed Description

Author

Emmanouil Stafilarakis

Mario Stanke

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

• include/types.hh
• src/types.cc