SEQALN_CONSTANTS Struct Reference

#include <seqaln.h>

List of all members.

Public Attributes
int	alpha
int	beta
int	csub
int	revcomp
int	cutoff
int	naligns
int	rptalign
int	rptmat
int	rptscore
int	rptptable
int	rpttrace
int	rptboth
int	verbose
int	width
int(*	deltafn )()
int	traceupper
int	envelope
int	flip
int	showmmatch
int	palpha
int	pbeta
int	overout
int	nsims
int	ndeclumps
int	allscores
double	gamma
double	p
char *	randfile
int	match
int	mismatch
int	xmatrix [32][32]
int	offset
int	window
int	center
int	Delta1
int	Delta2
int	Debug
enum PTYPE	ptype
enum STYPE	stype
enum MTYPE	mtype
enum BTYPE	btype
enum MEMUSE	memuse
enum STATS	stats

---

Member Data Documentation

int SEQALN_CONSTANTS::alpha

Referenced by fddeclump(), fitD(), fitS(), fsdeclump(), gap(), globalD(), globalS(), initmaxS(), localS(), lsdeclump(), overS(), parseargs(), parseargs_str_new(), pfitS(), pfsdeclump(), ptrace(), results_init(), rpt_row(), rpt_scores(), dyaln::setGapCost(), srlocalS(), srlsdeclump(), trace(), trlocalS(), trlsdeclump(), trrpt_scores(), and trtrace().

int SEQALN_CONSTANTS::beta

Referenced by fddeclump(), fitD(), fitS(), fsdeclump(), gap(), globalD(), globalS(), initmaxS(), localS(), lsdeclump(), overS(), parseargs(), parseargs_str_new(), pfitS(), pfsdeclump(), ptrace(), results_init(), rpt_row(), rpt_scores(), dyaln::setGapCost(), srlocalS(), srlsdeclump(), and trace().

int SEQALN_CONSTANTS::csub

Referenced by dyaln::initParameter(), norm_gen(), parseargs(), parseargs_str_new(), dyaln::setcsub(), and aln::setcsub().

int SEQALN_CONSTANTS::revcomp

Referenced by parseargs().

int SEQALN_CONSTANTS::cutoff

Referenced by main(), memfree(), dyaln::outputAln(), and parseargs().

int SEQALN_CONSTANTS::naligns

Referenced by getmaxS(), memfree(), parseargs(), pvlocalS(), results_init(), dyaln::setNaligns(), aln::setNaligns(), and srgetmaxS().

int SEQALN_CONSTANTS::rptalign

Referenced by dyaln::initParameter(), main(), dyaln::outputAln(), parseargs(), parseargs_str_new(), rpt_align(), rpt_alignment(), trrpt_alignment(), and mgsaln::while().

int SEQALN_CONSTANTS::rptmat

Referenced by fitD(), fitS(), globalD(), globalS(), dyaln::initParameter(), localS(), main(), dyaln::outputAln(), overS(), parseargs(), parseargs_str_new(), pfitS(), rpt_scores(), srlocalS(), trlocalS(), and trrpt_scores().

int SEQALN_CONSTANTS::rptscore

Referenced by dyaln::initParameter(), main(), dyaln::outputAln(), parseargs(), parseargs_str_new(), rpt_align(), rpt_alignment(), trrpt_alignment(), and mgsaln::while().

int SEQALN_CONSTANTS::rptptable

Referenced by getpvalue(), and parseargs().

int SEQALN_CONSTANTS::rpttrace

Referenced by dyaln::initParameter(), main(), dyaln::outputAln(), parseargs(), parseargs_str_new(), and mgsaln::while().

int SEQALN_CONSTANTS::rptboth

Referenced by dyaln::initParameter(), main(), dyaln::outputAln(), parseargs(), parseargs_str_new(), and mgsaln::while().

int SEQALN_CONSTANTS::verbose

Referenced by parseargs().

int SEQALN_CONSTANTS::width

Referenced by parseargs(), rpt_align(), rpt_alignment(), and trrpt_alignment().

int(* SEQALN_CONSTANTS::deltafn)()

(

)

Referenced by fddeclump(), fitD(), fitS(), fsdeclump(), globalD(), globalS(), loadDeltaFunction(), localS(), lsdeclump(), norm_gen(), overS(), parseargs(), parseargs_str_new(), pfitS(), pfsdeclump(), ptrace(), rpt_alignment(), srlocalS(), srlsdeclump(), tandem_gen(), topscore(), trace(), trlocalS(), trlsdeclump(), and trtrace().

int SEQALN_CONSTANTS::traceupper

Referenced by dyaln::initParameter(), main(), dyaln::outputAln(), parseargs(), parseargs_str_new(), print_trace(), ptrace(), trace(), trtrace(), and mgsaln::while().

int SEQALN_CONSTANTS::envelope

Referenced by dyaln::initParameter(), parseargs(), parseargs_str_new(), print_trace(), ptrace(), trace(), and trtrace().

int SEQALN_CONSTANTS::flip

Referenced by dyaln::initParameter(), parseargs(), parseargs_str_new(), and print_trace().

int SEQALN_CONSTANTS::showmmatch

Referenced by dyaln::initParameter(), norm_gen(), parseargs(), parseargs_str_new(), rpt_alignment(), tandem_gen(), and trrpt_alignment().

int SEQALN_CONSTANTS::palpha

Referenced by load_pro(), pfitS(), pfsdeclump(), ptrace(), and results_init().

int SEQALN_CONSTANTS::pbeta

Referenced by load_pro(), pfitS(), pfsdeclump(), and results_init().

int SEQALN_CONSTANTS::overout

Referenced by main(), and parseargs().

int SEQALN_CONSTANTS::nsims

Referenced by parseargs(), and results_init().

int SEQALN_CONSTANTS::ndeclumps

Referenced by parseargs(), pvlocalS(), pvsrlocalS(), and results_init().

int SEQALN_CONSTANTS::allscores

Referenced by getpvalue(), main(), and parseargs().

double SEQALN_CONSTANTS::gamma

Referenced by main(), and parseargs().

double SEQALN_CONSTANTS::p

Referenced by main(), and parseargs().

char * SEQALN_CONSTANTS::randfile

Referenced by main(), and parseargs().

int SEQALN_CONSTANTS::match

Referenced by delta(), parseargs(), parseargs_str_new(), and dyaln::setup().

int SEQALN_CONSTANTS::mismatch

Referenced by delta(), parseargs(), parseargs_str_new(), and dyaln::setup().

int SEQALN_CONSTANTS::xmatrix

Referenced by load_mat(), and mdelta().

int SEQALN_CONSTANTS::offset

Referenced by load_mat().

int SEQALN_CONSTANTS::window

Referenced by parseargs(), parseargs_str_new(), dyaln::setup(), and trrpt_alignment().

int SEQALN_CONSTANTS::center

int SEQALN_CONSTANTS::Delta1

int SEQALN_CONSTANTS::Delta2

int SEQALN_CONSTANTS::Debug

Referenced by fddeclump(), fsdeclump(), getpvalue(), dyaln::initParameter(), load_mat(), lsdeclump(), main(), nextpval(), norm_gen(), parseargs(), ptrace(), pvlocalS(), pvsrlocalS(), srlsdeclump(), tandem_gen(), topscore(), trace(), trlocalS(), trlsdeclump(), trrpt_alignment(), and trtrace().

enum PTYPE SEQALN_CONSTANTS::ptype

Referenced by dyaln::initParameter(), main(), markdiag(), norm_gen(), ptrace(), results_init(), rpt_alignment(), trace(), and trrpt_alignment().

enum STYPE SEQALN_CONSTANTS::stype

Referenced by dyaln::initParameter(), loadDeltaFunction(), main(), norm_gen(), parseargs(), parseargs_str_new(), pvlocalS(), pvsrlocalS(), results_init(), rpt_align(), rpt_alignment(), rpt_row(), rpt_scores(), dyaln::setup(), tandem_gen(), topscore(), and trrpt_alignment().

enum MTYPE SEQALN_CONSTANTS::mtype

Referenced by bestincol(), bestinrow(), gettop(), dyaln::initParameter(), load_mat(), main(), norm_gen(), parseargs(), parseargs_str_new(), results_init(), rpt_alignment(), dyaln::setGapCost(), dyaln::setup(), tandem_gen(), topscore(), and trrpt_scores().

enum BTYPE SEQALN_CONSTANTS::btype

Referenced by dyaln::align(), gen_align(), dyaln::initParameter(), main(), parseargs(), parseargs_str_new(), results_init(), rpt_row(), dyaln::setGapCost(), and dyaln::setup().

enum MEMUSE SEQALN_CONSTANTS::memuse

Referenced by fitD(), fitS(), globalD(), globalS(), dyaln::initParameter(), localS(), main(), norm_gen(), dyaln::outputAln(), dyaln::outputTab(), dyaln::outputTabPos(), overS(), parseargs(), pfitS(), prpt_row(), pvlocalS(), pvsrlocalS(), results_init(), rpt_align(), rpt_alignment(), rpt_row(), srlocalS(), tandem_gen(), trlocalS(), and mgsaln::while().

enum STATS SEQALN_CONSTANTS::stats

Referenced by main(), parseargs(), parseargs_str_new(), results_init(), and dyaln::setup().

---

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

• seqaln/seqaln/kzaln/seqaln.h
• seqaln/seqaln/src/seqaln.h