SEQALN_RESULTS Struct Reference

#include <seqaln.h>

List of all members.

Public Attributes
int **	S
int *	E
int *	F
int *	best
int	bestS
int	bestSi
int	bestSj
int	naligns
int	jstart
int	jmax
int	maxentry
SEQALN_TRACE *	trace
char **	aligned
char *	linbits
SEQALN_SIJ *	listsij
int	listcount
struct SEQALN_PVALUE *	pvalue
int	start1
int	start2
char *	align0
char *	align1
char *	align2
int	align_len
int	nogap_len
int	max_align_len
int	collen
int	rowlen
int	S_size
int	match_freq1 [26]
int	match_freq2 [26]
int	iden_count
int	siml_count
int	end1
int	end2

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Member Data Documentation

int ** SEQALN_RESULTS::S

Referenced by bestincol(), bestinrow(), fddeclump(), fitD(), fitS(), fsdeclump(), getmaxS(), getminS(), globalD(), globalS(), localS(), lsdeclump(), memfree(), overS(), pfitS(), pfsdeclump(), prpt_row(), ptrace(), pvlocalS(), pvsrlocalS(), results_init(), rpt_row(), rpt_scores(), srgetmaxS(), srlocalS(), srlsdeclump(), trace(), trlocalS(), trlsdeclump(), trrpt_scores(), and trtrace().

int * SEQALN_RESULTS::E

int * SEQALN_RESULTS::F

Referenced by fddeclump(), fitD(), fitS(), fsdeclump(), globalD(), globalS(), localS(), lsdeclump(), overS(), pfitS(), pfsdeclump(), pvlocalS(), pvsrlocalS(), results_init(), srlocalS(), and srlsdeclump().

int * SEQALN_RESULTS::best

Referenced by initmaxS(), results_init(), and srgetmaxS().

int SEQALN_RESULTS::bestS

Referenced by bestincol(), bestinrow(), fddeclump(), fitD(), fitS(), fsdeclump(), getmaxS(), getminS(), globalD(), globalS(), localS(), main(), nextpval(), dyaln::outputAln(), dyaln::outputTabPos(), overS(), pfitS(), pfsdeclump(), ptrace(), pvlocalS(), pvsrlocalS(), results_init(), rpt_align(), rpt_alignment(), srgetmaxS(), srlocalS(), trace(), trlocalS(), trlsdeclump(), trrpt_alignment(), and trtrace().

int SEQALN_RESULTS::bestSi

Referenced by bestincol(), bestinrow(), fddeclump(), fitD(), fitS(), fsdeclump(), getmaxS(), getminS(), globalD(), globalS(), localS(), overS(), pfitS(), pfsdeclump(), ptrace(), results_init(), rpt_align(), rpt_alignment(), srgetmaxS(), srlocalS(), trace(), trlocalS(), trlsdeclump(), trrpt_alignment(), and trtrace().

int SEQALN_RESULTS::bestSj

Referenced by bestincol(), bestinrow(), fddeclump(), fitD(), fitS(), fsdeclump(), getmaxS(), getminS(), globalD(), globalS(), localS(), main(), overS(), pfitS(), pfsdeclump(), ptrace(), results_init(), rpt_align(), rpt_alignment(), srgetmaxS(), srlocalS(), trace(), trlocalS(), trlsdeclump(), trrpt_alignment(), and trtrace().

int SEQALN_RESULTS::naligns

Referenced by main(), dyaln::outputAln(), pfsdeclump(), and results_init().

int SEQALN_RESULTS::jstart

int SEQALN_RESULTS::jmax

int SEQALN_RESULTS::maxentry

Referenced by initmaxS(), results_init(), and topscore().

SEQALN_TRACE * SEQALN_RESULTS::trace

Referenced by freeTraceList(), markdiag(), markseq(), norm_gen(), dyaln::outputTab(), dyaln::outputTabPos(), print_trace(), ptrace(), rpt_align(), rpt_alignment(), tandem_gen(), trace(), trrpt_alignment(), and trtrace().

char ** SEQALN_RESULTS::aligned

Referenced by fddeclump(), fsdeclump(), getmaxS(), lsdeclump(), markdiag(), memfree(), pfsdeclump(), prpt_row(), ptrace(), pvlocalS(), pvsrlocalS(), results_init(), rpt_row(), rpt_scores(), srgetmaxS(), srlsdeclump(), and trace().

char * SEQALN_RESULTS::linbits

Referenced by markseq(), results_init(), rpt_row(), trlsdeclump(), and trrpt_scores().

SEQALN_SIJ * SEQALN_RESULTS::listsij

int SEQALN_RESULTS::listcount

struct SEQALN_PVALUE * SEQALN_RESULTS::pvalue [read]

Referenced by getpvalue(), main(), nextpval(), parseargs(), parseargs_str_new(), pvlocalS(), pvsrlocalS(), results_init(), and dyaln::setup().

int SEQALN_RESULTS::start1

Referenced by dyaln::isSimple(), norm_gen(), dyaln::outputTab(), dyaln::outputTabPos(), rpt_align(), tandem_gen(), and trace().

int SEQALN_RESULTS::start2

Referenced by dyaln::isSimple(), norm_gen(), dyaln::outputTab(), dyaln::outputTabPos(), rpt_align(), tandem_gen(), and trace().

char * SEQALN_RESULTS::align0

Referenced by norm_gen(), rpt_align(), and tandem_gen().

char * SEQALN_RESULTS::align1

Referenced by norm_gen(), dyaln::outputTab(), dyaln::outputTabPos(), rpt_align(), and tandem_gen().

char * SEQALN_RESULTS::align2

Referenced by norm_gen(), dyaln::outputTab(), dyaln::outputTabPos(), rpt_align(), and tandem_gen().

int SEQALN_RESULTS::align_len

Referenced by norm_gen(), dyaln::outputTab(), dyaln::outputTabPos(), ptrace(), rpt_align(), tandem_gen(), trace(), and trtrace().

int SEQALN_RESULTS::nogap_len

Referenced by norm_gen(), dyaln::outputTab(), and dyaln::outputTabPos().

int SEQALN_RESULTS::max_align_len

Referenced by norm_gen(), and dyaln::setup().

int SEQALN_RESULTS::collen

Referenced by dyaln::setup().

int SEQALN_RESULTS::rowlen

Referenced by dyaln::setup().

int SEQALN_RESULTS::S_size

Referenced by dyaln::setup().

int SEQALN_RESULTS::match_freq1

Referenced by norm_gen(), dyaln::outputTab(), and dyaln::outputTabPos().

int SEQALN_RESULTS::match_freq2

Referenced by norm_gen(), dyaln::outputTab(), and dyaln::outputTabPos().

int SEQALN_RESULTS::iden_count

Referenced by norm_gen(), dyaln::outputTab(), and dyaln::outputTabPos().

int SEQALN_RESULTS::siml_count

Referenced by norm_gen(), dyaln::outputTab(), and dyaln::outputTabPos().

int SEQALN_RESULTS::end1

Referenced by dyaln::isSimple(), dyaln::outputTab(), and dyaln::outputTabPos().

int SEQALN_RESULTS::end2

Referenced by dyaln::isSimple(), dyaln::outputTab(), and dyaln::outputTabPos().

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

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