arb_dnarates.cxx File Reference

#include "DNAml_rates_1_0.h"
#include <aw_awar_defs.hxx>
#include <unistd.h>
#include <cmath>

Include dependency graph for arb_dnarates.cxx:

Go to the source code of this file.

Macros
#define	programName   "DNAml_rates"
#define	programVersion   "1.0.0"
#define	programDate   "April 11, 1992"
#define	assert(bed)   arb_assert(bed)

Functions
static void	getnums (FILE *INFILE)
int	min (int i, int j)
bool	digit (int ch)
bool	white (int ch)
static void	uppercase (int *chptr)
static int	base36 (int ch)
static int	itobase36 (int i)
static int	findch (int c, FILE *INFILE)
static void	inputweights (FILE *INFILE)
static void	getoptions (FILE *INFILE)
static void	getbasefreqs (FILE *INFILE)
static void	getyspace ()
static void	setuptree (tree *tr, const int numSp)
static void	freeTreeNode (nodeptr p)
static void	freeTree (tree *tr)
static void	getdata (tree *tr, FILE *INFILE)
static void	sitesort ()
static void	sitecombcrunch ()
static void	makeweights ()
static void	makevalues (tree *tr)
static void	empiricalfreqs (tree *tr)
static void	getinput (tree *tr, FILE *INFILE)
static xarray *	setupxarray ()
static void	linkxarray (int req, int min, xarray **freexptr, xarray **usedxptr)
static void	setupnodex (tree *tr)
static xarray *	getxtip (nodeptr p)
static xarray *	getxnode (nodeptr p)
static void	newview (nodeptr p)
static void	hookup (nodeptr p, nodeptr q, double z)
static void	initrav (nodeptr p)
static int	treeFinishCom (FILE *INFILE)
static int	treeGetCh (FILE *INFILE)
static void	treeFlushLabel (FILE *INFILE)
static int	findTipName (tree *tr, int ch, FILE *INFILE)
static double	processLength (FILE *INFILE)
static void	treeFlushLen (FILE *INFILE)
static void	treeNeedCh (int c1, const char *where, FILE *INFILE)
static void	addElementLen (tree *tr, nodeptr p, FILE *INFILE)
static void	uprootTree (tree *tr, nodeptr p)
static void	treeReadLen (tree *tr, FILE *INFILE)
static double	evaluate (tree *tr, nodeptr p)
static void	dli_dki (nodeptr p)
static void	spanSubtree (nodeptr p)
static void	findSiteRates (tree *tr, double ki_min, double ki_max, double d_ki, double max_error)
static double	subtreeLength (nodeptr p)
static double	treeLength (tree *tr)
static void	categorize (int Sites, int Categs, int Weight[], int Pattern[], double Patrate[], double categrate[], int sitecateg[])
static void	getArbFilter ()
static int	get_next_SAI_count ()
static GBDATA *	create_next_SAI ()
static bool	writeToArb ()
static void	openArb (const char *dbname)
static void	saveArb (const char *saveAs)
static void	closeArb ()
static void	wrfile (FILE *outfile, int Sites, int Categs, int Weight[], double categrate[], int sitecateg[])
static void	summarize (int treenum)
static void	makeUserRates (tree *tr, FILE *INFILE)
bool	is_char (const char *name, char c)
bool	wantSTDIN (const char *iname)
int	ARB_main (int argc, char *argv[])

Variables
static xarray *	usedxtip
static xarray *	freextip
static double	dLidki [maxpatterns]
static double	bestki [maxpatterns]
static double	bestLi [maxpatterns]
static double	patrate [maxpatterns]
static double	xi
static double	xv
static double	ttratio
static double	freqa
static double	freqc
static double	freqg
static double	freqt
static double	freqr
static double	freqy
static double	invfreqr
static double	invfreqy
static double	freqar
static double	freqcy
static double	freqgr
static double	freqty
static double	fracchange
static int	info [maxsites+1]
static int	patsite [maxsites+1]
static int	pattern [maxsites+1]
static int	patweight [maxsites+1]
static int	weight [maxsites+1]
static int	categs
static int	endsite
static int	mininfo
static int	numsp
static int	sites
static int	weightsum
static bool	anerror
static bool	freqsfrom
static bool	interleaved
static bool	printdata
static bool	writefile
static bool	userweights
static char *	y [maxsp+1]
static char *	arb_filter
static char *	alignment_name
static GBDATA *	gb_main

Macro Definition Documentation

#define programName   "DNAml_rates"

Definition at line 25 of file arb_dnarates.cxx.

Referenced by getnums().

#define programVersion   "1.0.0"

Definition at line 26 of file arb_dnarates.cxx.

Referenced by getnums().

#define programDate   "April 11, 1992"

Definition at line 27 of file arb_dnarates.cxx.

Referenced by getnums().

#define assert

(

bed

)

arb_assert(bed)

Definition at line 36 of file arb_dnarates.cxx.

Referenced by addElementLen(), createAttribList(), createColormap(), createOriginRNS(), createVisualInfo(), initBaseLookups(), Initialize(), mutateRNS(), newSpreading(), randProb(), randval(), and spreadRand().

Function Documentation

static void getnums ( FILE *  INFILE )

static

Definition at line 87 of file arb_dnarates.cxx.

References anerror, maxsites, maxsp, numsp, programDate, programName, programVersion, and sites.

Referenced by getinput().

int min ( int  i, int  j  )

inline

Definition at line 122 of file arb_dnarates.cxx.

Referenced by wrfile().

bool digit ( int  ch )

inline

Definition at line 123 of file arb_dnarates.cxx.

Referenced by getdata(), and PH_create_ml_multiline_SAI().

bool white ( int  ch )

inline

Definition at line 124 of file arb_dnarates.cxx.

Referenced by getdata(), inputweights(), only_whitespace(), and treeGetCh().

static void uppercase ( int *  chptr )

static

Definition at line 126 of file arb_dnarates.cxx.

Referenced by getdata(), and getoptions().

static int base36 ( int  ch )

static

Definition at line 138 of file arb_dnarates.cxx.

Referenced by get_short(), and inputweights().

static int itobase36 ( int  i )

static

Definition at line 150 of file arb_dnarates.cxx.

Referenced by getdata(), wrfile(), and writeToArb().

static int findch ( int  c, FILE *  INFILE  )

static

Definition at line 160 of file arb_dnarates.cxx.

Referenced by getbasefreqs(), getoptions(), inputweights(), makeUserRates(), and treeFlushLabel().

static void inputweights ( FILE *  INFILE )

static

Definition at line 167 of file arb_dnarates.cxx.

References anerror, base36(), findch(), nmlngth, sites, weight, weightsum, and white().

Referenced by getoptions().

static void getoptions ( FILE *  INFILE )

static

Definition at line 195 of file arb_dnarates.cxx.

References anerror, categs, findch(), freqsfrom, inputweights(), interleaved, maxcategories, MIN_INFO, mininfo, numsp, printdata, sites, ttratio, uppercase(), userweights, weight, weightsum, and writefile.

Referenced by getinput().

static void getbasefreqs ( FILE *  INFILE )

static

Definition at line 337 of file arb_dnarates.cxx.

References anerror, findch(), fracchange, freqa, freqar, freqc, freqcy, freqg, freqgr, freqr, freqsfrom, freqt, freqty, freqy, invfreqr, invfreqy, ttratio, xi, and xv.

Referenced by getinput().

static void getyspace ( )

static

Definition at line 381 of file arb_dnarates.cxx.

References anerror, numsp, sites, and y.

Referenced by getinput().

static void setuptree ( tree *  tr, const int  numSp  )

static

Definition at line 398 of file arb_dnarates.cxx.

References anerror, node::back, leafs_2_nodes(), tree::likelihood, tree::mxtips, node::next, tree::nextnode, tree::nodep, tree::ntips, NULp, node::number, tree::opt_level, ROOTED, tree::smoothed, tree::start, node::tip, unlikely, and node::x.

Referenced by getinput().

static void freeTreeNode ( nodeptr  p )

static

Definition at line 445 of file arb_dnarates.cxx.

References xarray::a, and node::x.

Referenced by freeTree().

static void freeTree ( tree *  tr )

static

Definition at line 456 of file arb_dnarates.cxx.

References freeTreeNode(), leafs_2_nodes(), tree::mxtips, node::next, tree::nodep, and ROOTED.

Referenced by ARB_main().

static void getdata ( tree *  tr, FILE *  INFILE  )

static

Definition at line 476 of file arb_dnarates.cxx.

References anerror, digit(), info, interleaved, itobase36(), MIN_INFO, node::name, nmlngth, tree::nodep, numsp, printdata, sites, uppercase(), userweights, weight, white(), and y.

Referenced by getinput().

static void sitesort ( )

static

Definition at line 650 of file arb_dnarates.cxx.

References numsp, patsite, sites, and y.

Referenced by makeweights().

static void sitecombcrunch ( )

static

Definition at line 680 of file arb_dnarates.cxx.

References endsite, numsp, patsite, pattern, patweight, sites, weight, and y.

Referenced by makeweights().

static void makeweights ( )

static

Definition at line 712 of file arb_dnarates.cxx.

References anerror, endsite, maxpatterns, patsite, sitecombcrunch(), sites, and sitesort().

Referenced by getinput().

static void makevalues ( tree *  tr )

static

Definition at line 728 of file arb_dnarates.cxx.

References endsite, tree::nodep, numsp, patsite, node::tip, and y.

Referenced by getinput().

static void empiricalfreqs ( tree *  tr )

static

Definition at line 740 of file arb_dnarates.cxx.

References endsite, freqa, freqc, freqg, freqt, tree::nodep, numsp, patweight, and node::tip.

Referenced by getinput().

static void getinput ( tree *  tr, FILE *  INFILE  )

static

Definition at line 784 of file arb_dnarates.cxx.

References anerror, empiricalfreqs(), freqsfrom, getbasefreqs(), getdata(), getnums(), getoptions(), getyspace(), makevalues(), makeweights(), numsp, and setuptree().

Referenced by ARB_main().

static xarray* setupxarray ( )

static

Definition at line 802 of file arb_dnarates.cxx.

References xarray::a, xarray::c, endsite, xarray::g, xarray::next, NULp, xarray::owner, xarray::prev, and xarray::t.

Referenced by linkxarray(), and setupnodex().

static void linkxarray ( int  req, int  min, xarray **  freexptr, xarray **  usedxptr  )

static

Definition at line 823 of file arb_dnarates.cxx.

References anerror, xarray::next, NULp, xarray::prev, and setupxarray().

Referenced by ARB_main().

static void setupnodex ( tree *  tr )

static

Definition at line 860 of file arb_dnarates.cxx.

References anerror, tree::mxtips, tree::nodep, setupxarray(), and node::x.

Referenced by ARB_main().

static xarray* getxtip ( nodeptr  p )

static

Definition at line 868 of file arb_dnarates.cxx.

References anerror, freextip, xarray::next, NULp, xarray::owner, xarray::prev, usedxtip, and node::x.

Referenced by newview().

static xarray* getxnode ( nodeptr  p )

static

Definition at line 932 of file arb_dnarates.cxx.

References node::next, NULp, s, and node::x.

Referenced by newview().

static void newview ( nodeptr  p )

static

Definition at line 949 of file arb_dnarates.cxx.

References xarray::a, node::back, xarray::c, endsite, freqa, freqc, freqg, freqt, xarray::g, getxnode(), getxtip(), invfreqr, invfreqy, node::next, patrate, xarray::t, node::tip, node::x, xv, node::z, and zmin.

Referenced by dli_dki(), evaluate(), and initrav().

static void hookup ( nodeptr  p, nodeptr  q, double  z  )

static

Definition at line 1054 of file arb_dnarates.cxx.

References node::back, and node::z.

Referenced by addElementLen(), and uprootTree().

static void initrav ( nodeptr  p )

static

Definition at line 1061 of file arb_dnarates.cxx.

References node::back, newview(), node::next, and node::tip.

Referenced by findSiteRates(), and treeReadLen().

static int treeFinishCom ( FILE *  INFILE )

static

Definition at line 1073 of file arb_dnarates.cxx.

References inquote.

Referenced by treeGetCh().

static int treeGetCh ( FILE *  INFILE )

static

Definition at line 1087 of file arb_dnarates.cxx.

References treeFinishCom(), and white().

Referenced by addElementLen(), processLength(), treeFlushLabel(), treeFlushLen(), treeNeedCh(), and treeReadLen().

static void treeFlushLabel ( FILE *  INFILE )

static

Definition at line 1102 of file arb_dnarates.cxx.

References findch(), and treeGetCh().

Referenced by addElementLen(), and treeReadLen().

static int findTipName ( tree *  tr, int  ch, FILE *  INFILE  )

static

Definition at line 1129 of file arb_dnarates.cxx.

References node::back, tree::mxtips, node::name, nmlngth, and tree::nodep.

Referenced by addElementLen().

static double processLength ( FILE *  INFILE )

static

Definition at line 1195 of file arb_dnarates.cxx.

References anerror, and treeGetCh().

Referenced by addElementLen(), and treeFlushLen().

static void treeFlushLen ( FILE *  INFILE )

static

Definition at line 1214 of file arb_dnarates.cxx.

References processLength(), and treeGetCh().

Referenced by treeReadLen().

static void treeNeedCh ( int  c1, const char *  where, FILE *  INFILE  )

static

Definition at line 1222 of file arb_dnarates.cxx.

References anerror, and treeGetCh().

Referenced by addElementLen(), and treeReadLen().

static void addElementLen ( tree *  tr, nodeptr  p, FILE *  INFILE  )

static

Definition at line 1239 of file arb_dnarates.cxx.

References anerror, assert, findTipName(), fracchange, hookup(), tree::mxtips, node::next, tree::nextnode, tree::nodep, tree::ntips, node::number, processLength(), tree::rooted, tree::start, treeFlushLabel(), treeGetCh(), treeNeedCh(), and zmax.

Referenced by treeReadLen().

static void uprootTree ( tree *  tr, nodeptr  p  )

static

Definition at line 1281 of file arb_dnarates.cxx.

References anerror, node::back, hookup(), tree::mxtips, node::next, tree::nextnode, tree::nodep, tree::ntips, NULp, tree::rooted, s, node::tip, and node::z.

Referenced by treeReadLen().

static void treeReadLen ( tree *  tr, FILE *  INFILE  )

static

Definition at line 1317 of file arb_dnarates.cxx.

References addElementLen(), anerror, node::back, initrav(), tree::mxtips, node::next, tree::nextnode, tree::nodep, tree::ntips, NULp, tree::opt_level, tree::rooted, tree::smoothed, tree::start, treeFlushLabel(), treeFlushLen(), treeGetCh(), treeNeedCh(), and uprootTree().

Referenced by makeUserRates().

static double evaluate ( tree *  tr, nodeptr  p  )

static

Definition at line 1370 of file arb_dnarates.cxx.

References xarray::a, node::back, xarray::c, endsite, freqa, freqc, freqg, freqt, xarray::g, invfreqr, invfreqy, tree::likelihood, tree::log_f, newview(), patrate, patweight, xarray::t, node::x, xv, node::z, and zmin.

Referenced by findSiteRates().

static void dli_dki ( nodeptr  p )

static

Definition at line 1432 of file arb_dnarates.cxx.

References xarray::a, node::back, xarray::c, dLidki, endsite, freqa, freqc, freqg, freqt, xarray::g, invfreqr, invfreqy, newview(), patrate, patweight, xarray::t, node::x, xv, node::z, and zmin.

Referenced by spanSubtree().

static void spanSubtree ( nodeptr  p )

static

Definition at line 1488 of file arb_dnarates.cxx.

References node::back, dli_dki(), node::next, and node::tip.

Referenced by findSiteRates().

static void findSiteRates ( tree *  tr, double  ki_min, double  ki_max, double  d_ki, double  max_error  )

static

Definition at line 1498 of file arb_dnarates.cxx.

References anerror, node::back, bestki, bestLi, dLidki, endsite, evaluate(), initrav(), tree::log_f, node::next, patrate, spanSubtree(), tree::start, node::tip, and unlikely.

Referenced by makeUserRates().

static double subtreeLength ( nodeptr  p )

static

Definition at line 1559 of file arb_dnarates.cxx.

References node::back, fracchange, node::next, node::tip, and node::z.

Referenced by treeLength().

static double treeLength ( tree *  tr )

static

Definition at line 1570 of file arb_dnarates.cxx.

References node::back, node::next, tree::start, subtreeLength(), and node::tip.

Referenced by makeUserRates().

static void categorize ( int  Sites, int  Categs, int  Weight[], int  Pattern[], double  Patrate[], double  categrate[], int  sitecateg[]  )

static

Definition at line 1581 of file arb_dnarates.cxx.

References nint.

Referenced by summarize(), and writeToArb().

static void getArbFilter ( )

static

Get the calling filter, needed to expand weights afterwards

Definition at line 1643 of file arb_dnarates.cxx.

References AWAR_GDE_EXPORT_FILTER, GB_begin_transaction(), GB_commit_transaction(), GBT_get_default_alignment(), and GBT_read_string().

Referenced by ARB_main().

static int get_next_SAI_count ( )

static

Definition at line 1651 of file arb_dnarates.cxx.

References GB_FIND, GB_INT, GB_read_int(), GB_search(), and GB_write_int().

Referenced by create_next_SAI().

static GBDATA* create_next_SAI ( )

static

Definition at line 1662 of file arb_dnarates.cxx.

References GBT_find_or_create_SAI(), GBT_find_SAI(), get_next_SAI_count(), and NULp.

Referenced by writeToArb().

static bool writeToArb ( )

static

Definition at line 1678 of file arb_dnarates.cxx.

References categorize(), categs, create_next_SAI(), error(), GB_await_error(), GB_begin_transaction(), GB_end_transaction(), GB_FLOATS, GB_STRING, GB_write_floats(), GB_write_string(), GBS_global_string(), GBT_add_data(), GBT_get_alignment_len(), itobase36(), KI_MAX, maxcategories, maxsites, NULp, patrate, pattern, sites, and weight.

Referenced by ARB_main().

static void openArb ( const char *  dbname )

static

Definition at line 1776 of file arb_dnarates.cxx.

References EXIT_FAILURE, GB_open(), GB_warning(), and GB_warningf().

Referenced by ARB_main().

static void saveArb ( const char *  saveAs )

static

Definition at line 1789 of file arb_dnarates.cxx.

References error(), EXIT_FAILURE, GB_save(), and GB_warningf().

Referenced by ARB_main().

static void closeArb ( )

static

Definition at line 1797 of file arb_dnarates.cxx.

References GB_close().

Referenced by ARB_main().

static void wrfile ( FILE *  outfile, int  Sites, int  Categs, int  Weight[], double  categrate[], int  sitecateg[]  )

static

Definition at line 1801 of file arb_dnarates.cxx.

References itobase36(), and min().

Referenced by summarize().

static void summarize ( int  treenum )

static

Definition at line 1847 of file arb_dnarates.cxx.

References categorize(), categs, maxcategories, maxsites, patrate, pattern, sites, weight, wrfile(), and writefile.

Referenced by makeUserRates().

static void makeUserRates ( tree *  tr, FILE *  INFILE  )

static

Definition at line 1891 of file arb_dnarates.cxx.

References anerror, endsite, findch(), findSiteRates(), KI_MAX, MAX_ERROR, tree::ntips, patrate, RATE_STEP, summarize(), treeLength(), and treeReadLen().

Referenced by ARB_main().

bool is_char ( const char *  name, char  c  )

inline

Definition at line 1920 of file arb_dnarates.cxx.

Referenced by wantSTDIN().

bool wantSTDIN ( const char *  iname )

inline

Definition at line 1921 of file arb_dnarates.cxx.

References is_char().

Referenced by ARB_main().

int ARB_main	(	int	argc,
		char *	argv[]
	)

Definition at line 1923 of file arb_dnarates.cxx.

References anerror, AWAR_GDE_EXPORT_FILTER, closeArb(), error(), EXIT_FAILURE, EXIT_SUCCESS, fputs(), freeTree(), freextip, GB_IO_error(), getArbFilter(), getinput(), help(), linkxarray(), makeUserRates(), MAXNODES, tree::nodep, NULp, openArb(), saveArb(), setupnodex(), usedxtip, wantSTDIN(), and writeToArb().

Variable Documentation

xarray* usedxtip

static

Definition at line 41 of file arb_dnarates.cxx.

Referenced by ARB_main(), and getxtip().

xarray * freextip

static

Definition at line 41 of file arb_dnarates.cxx.

Referenced by ARB_main(), and getxtip().

double dLidki[maxpatterns]

static

Definition at line 44 of file arb_dnarates.cxx.

Referenced by dli_dki(), and findSiteRates().

double bestki[maxpatterns]

static

Definition at line 44 of file arb_dnarates.cxx.

Referenced by findSiteRates().

double bestLi[maxpatterns]

static

Definition at line 44 of file arb_dnarates.cxx.

Referenced by findSiteRates().

double patrate[maxpatterns]

static

Definition at line 44 of file arb_dnarates.cxx.

Referenced by dli_dki(), evaluate(), findSiteRates(), makeUserRates(), newview(), summarize(), and writeToArb().

double xi

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by AW_option_menu_struct::AW_option_menu_struct(), combak_(), comhes_(), comlr2_(), comlr_(), comqr2_(), comqr_(), csroot_(), getbasefreqs(), GEN_root::paint(), and AW_device::text_overlay().

double xv

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by dli_dki(), evaluate(), getbasefreqs(), and newview().

double ttratio

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by ColumnStat::get_ttratio(), getbasefreqs(), and getoptions().

double freqa

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by dli_dki(), empiricalfreqs(), evaluate(), getbasefreqs(), and newview().

double freqc

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by dli_dki(), empiricalfreqs(), evaluate(), getbasefreqs(), and newview().

double freqg

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by dli_dki(), empiricalfreqs(), evaluate(), getbasefreqs(), and newview().

double freqt

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by dli_dki(), empiricalfreqs(), evaluate(), getbasefreqs(), and newview().

double freqr

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by getbasefreqs().

double freqy

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by getbasefreqs().

double invfreqr

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by dli_dki(), evaluate(), getbasefreqs(), and newview().

double invfreqy

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by dli_dki(), evaluate(), getbasefreqs(), and newview().

double freqar

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by getbasefreqs().

double freqcy

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by getbasefreqs().

double freqgr

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by getbasefreqs().

double freqty

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by getbasefreqs().

double fracchange

static

Definition at line 50 of file arb_dnarates.cxx.

Referenced by addElementLen(), getbasefreqs(), and subtreeLength().

int info[maxsites+1]

static

Definition at line 57 of file arb_dnarates.cxx.

Referenced by InfoWindowRegistry::allocate_detach_id(), ARB_zfclose(), ST_ML::count_species_in_tree(), create_concatInfo_SAI(), QUERY::DbQuery_update_list(), del_short(), destroy_ColumnQualityInfo(), AWT_tree_selection::fill(), InfoWindowRegistry::find_maininfo_of_same_type_as(), InfoWindowRegistry::find_reusable_of_same_type_as(), g_b_undo_info(), get_short(), getdata(), getHitInfo(), Structure3D::GetSecondaryStructureInfo(), insert_interruption_to_macro_cb(), pngLoadF(), refresh_availfield_selbox_cb(), SET_QUERIED(), st_ml_add_quality_string_to_species(), and st_ml_add_sequence_part_to_stat().

int patsite[maxsites+1]

static

Definition at line 57 of file arb_dnarates.cxx.

Referenced by makevalues(), makeweights(), sitecombcrunch(), and sitesort().

int pattern[maxsites+1]

static

Definition at line 57 of file arb_dnarates.cxx.

Referenced by ED4_search_cb(), SearchTree::SearchTree(), sitecombcrunch(), summarize(), and writeToArb().

int patweight[maxsites+1]

static

Definition at line 57 of file arb_dnarates.cxx.

Referenced by dli_dki(), empiricalfreqs(), evaluate(), and sitecombcrunch().

int weight[maxsites+1]

static

Definition at line 57 of file arb_dnarates.cxx.

Referenced by ARB_main(), DeconstructedTree::deconstruct_weighted(), getdata(), getoptions(), inputweights(), sitecombcrunch(), summarize(), and writeToArb().

int categs

static

Definition at line 64 of file arb_dnarates.cxx.

Referenced by getoptions(), summarize(), and writeToArb().

int endsite

static

Definition at line 64 of file arb_dnarates.cxx.

Referenced by dli_dki(), empiricalfreqs(), evaluate(), findSiteRates(), makeUserRates(), makevalues(), makeweights(), newview(), setupxarray(), and sitecombcrunch().

int mininfo

static

Definition at line 64 of file arb_dnarates.cxx.

Referenced by getoptions().

int numsp

static

Definition at line 64 of file arb_dnarates.cxx.

Referenced by empiricalfreqs(), getdata(), getinput(), getnums(), getoptions(), getyspace(), makevalues(), sitecombcrunch(), and sitesort().

int sites

static

Definition at line 64 of file arb_dnarates.cxx.

Referenced by getdata(), getnums(), getoptions(), getyspace(), inputweights(), makeweights(), sitecombcrunch(), sitesort(), summarize(), and writeToArb().

int weightsum

static

Definition at line 64 of file arb_dnarates.cxx.

Referenced by getoptions(), and inputweights().

bool anerror

static

Definition at line 72 of file arb_dnarates.cxx.

Referenced by addElementLen(), ARB_main(), findSiteRates(), getbasefreqs(), getdata(), getinput(), getnums(), getoptions(), getxtip(), getyspace(), inputweights(), linkxarray(), makeUserRates(), makeweights(), processLength(), setupnodex(), setuptree(), treeNeedCh(), treeReadLen(), and uprootTree().

bool freqsfrom

static

Definition at line 72 of file arb_dnarates.cxx.

Referenced by getbasefreqs(), getinput(), and getoptions().

bool interleaved

static

Definition at line 72 of file arb_dnarates.cxx.

Referenced by getdata(), and getoptions().

bool printdata

static

Definition at line 72 of file arb_dnarates.cxx.

Referenced by getdata(), and getoptions().

bool writefile

static

Definition at line 72 of file arb_dnarates.cxx.

Referenced by getoptions(), and summarize().

bool userweights

static

Definition at line 72 of file arb_dnarates.cxx.

Referenced by getdata(), and getoptions().

char* y[maxsp+1]

static

Definition at line 80 of file arb_dnarates.cxx.

Referenced by AW_window::at_y(), AW_window::auto_increment(), AW_window::auto_space(), AW_displayColorRange(), AW_xfig::AW_xfig(), awt_aps_calc_pages_needed(), awt_aps_go(), awt_aps_set_magnification_to_fit_ypage(), awt_aps_text_changed(), UNTYPED::awt_create_collect_buttons(), awt_create_input_mask(), UNTYPED::awt_create_order_buttons(), buildColumnTranslatorFromAwars(), ED4_abstract_sequence_terminal::calc_interval_displayed_in_rectangle(), ED4_abstract_sequence_terminal::calc_update_interval(), DI_MATRIX::calculate(), ED4_base::check_all(), cinvit_(), ED4_base::clear_background(), AW_clipable::clip(), DI_MATRIX::compress(), ComputeRotationXY(), AP_userdef_matrix::create_awars(), create_helix_props_window(), AP_userdef_matrix::create_input_fields(), create_key_map_window(), create_matrix_config_window(), ItemFieldShader::customize(), detectEqualRowsAndColumns(), PH_display::display(), ED4_text_terminal::draw(), ED4_CursorShape::ED4_CursorShape(), elmhes_(), ED4_root::generate_window(), ALI_PATHMAP::get(), ED4_CursorShape::get_bounding_box(), ED4_manager::get_competent_child(), ED4_manager::get_competent_clicked_child(), get_max_slider_xpos(), get_max_slider_ypos(), get_upper_lower_cursor_pos(), ED4_scrolled_rectangle::get_world_rect(), getdata(), getyspace(), HalfSize(), highlight_and_update(), hqr2_(), hqr_(), invit_(), ED4_cursor::is_completely_visible(), ED4_cursor::is_partly_visible(), AW::Rectangle::left_edge(), SymmetricMatrixMapper::linear_index(), ED4_scrolled_rectangle::link(), AW::Rectangle::lower_left_corner(), makevalues(), matrix_config_changed_cb(), minfit_(), AP_userdef_matrix::normize(), GEN_root::paint(), ALI_PATHMAP::print(), AW_xfig::print(), probe_match(), qzvec_(), reduc2_(), reduc_(), Resize(), AW::Rectangle::right_edge(), SAI_init_calculator_awars(), ALI_PATHMAP::set(), ED4_cursor::set_abs_x(), MP_Main::set_p_eval(), ED4_manager::Show(), ED4_cursor::ShowCursor(), sitecombcrunch(), sitesort(), Structure3D::StoreCoordinates(), Structure3D::StoreHelixNrInfo(), svd_(), AP_userdef_matrix::update_from_awars(), and ED4_window::update_window_coords().

char* arb_filter

static

Definition at line 1639 of file arb_dnarates.cxx.

char* alignment_name

static

Definition at line 1640 of file arb_dnarates.cxx.

Referenced by calculateEndPosition(), colstat_2_gnuplot_cb(), FastAligner_start(), ALI_selection::fill(), ED4_root::get_alignment_name(), BI_helix::init(), NT_count_different_chars(), SQ_evaluate(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), SQ_pass2_no_tree(), st_ok_cb(), and translateSAItoColors().

GBDATA* gb_main

static

Definition at line 1641 of file arb_dnarates.cxx.