--- a/include/draw.h +++ b/include/draw.h @@ -116,19 +116,19 @@ #ifndef X_DISPLAY_MISSING -Display *display; /* the X display */ +extern Display *display; /* the X display */ extern Window mainwin; /* the main display window */ -int x, y; /* the corner of the window */ -unsigned int width, height; /* the width and height of the window */ +extern int x, y; /* the corner of the window */ +extern unsigned int width, height; /* the width and height of the window */ #define FONT "-*-new century schoolbook-medium-r-*-*-14-*" -char *fontrsc; /* the font resource */ -XFontStruct *fontst; /* the font strcture for the font */ -XGCValues gcv; /* graphics context values */ -GC gc1; /* a graphics context */ -XtAppContext appcontext; -Widget toplevel; -int nargc; -char** nargv; +extern char *fontrsc; /* the font resource */ +extern XFontStruct *fontst; /* the font strcture for the font */ +extern XGCValues gcv; /* graphics context values */ +extern GC gc1; /* a graphics context */ +extern XtAppContext appcontext; +extern Widget toplevel; +extern int nargc; +extern char** nargv; extern String res[16]; #define DEFGEOMETRY "600x400+20+50" --- a/include/phylip.h +++ b/include/phylip.h @@ -349,7 +349,8 @@ extern AjPFile embossancfile; extern AjPFile embossmixfile; extern AjPFile embossfactfile; -extern long spp, words, bits; +extern AjPPhyloState* phylostates; +extern long spp, words, bits, outgrno; extern boolean ibmpc, ansi, tranvsp; extern naym *nayme; /* names of species */ --- a/src/clique.c +++ b/src/clique.c @@ -9,7 +9,6 @@ #define FormWide 80 /* width of outfile page */ -AjPPhyloState* phylostates; AjPPhyloProp phyloanc = NULL; AjPPhyloProp phylofact = NULL; AjPPhyloProp phyloweights = NULL; @@ -72,10 +71,8 @@ Char infilename[FNMLNGTH], ancfilename[FNMLNGTH], factfilename[FNMLNGTH], weightfilename[FNMLNGTH]; const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; -long ActualChars, Cliqmin, outgrno, +long ActualChars, Cliqmin, col, ith, msets, setsz; boolean ancvar, Clmin, Factors, outgropt, trout, weights, noroot, justwts, printcomp, progress, treeprint, mulsets, firstset; --- a/src/cons.c +++ b/src/cons.c @@ -6,7 +6,7 @@ Char intreename[FNMLNGTH], intree2name[FNMLNGTH]; node *root; -long numopts, outgrno, col, setsz; +long numopts, col, setsz; long maxgrp; /* max. no. of groups in all trees found */ boolean trout, firsttree, noroot, outgropt, didreroot, prntsets, --- a/src/consense.c +++ b/src/consense.c @@ -19,8 +19,6 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; long trees_in; --- a/src/contml.c +++ b/src/contml.c @@ -69,10 +69,8 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; -long nonodes2, loci, totalleles, df, outgrno, col, +long nonodes2, loci, totalleles, df, col, datasets, ith, njumble, jumb=0; long inseed, inseed0; long *alleles, *locus, *weight; --- a/src/contrast.c +++ b/src/contrast.c @@ -40,7 +40,6 @@ const char* outfilename; -AjPFile embossoutfile; --- a/src/discboot.c +++ b/src/discboot.c @@ -56,7 +56,6 @@ const char* outfilename; -AjPFile embossoutfile; const char* outweightfilename; AjPFile embossoutweightfile; --- a/src/disc.c +++ b/src/disc.c @@ -1,7 +1,6 @@ #include "phylip.h" #include "disc.h" -AjPPhyloState* phylostates; /* version 3.6. (c) Copyright 1993-2002 by the University of Washington. Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe. --- a/src/discrete.c +++ b/src/discrete.c @@ -6,7 +6,7 @@ Permission is granted to copy and use this program provided no fee is charged for it and provided that this copyright notice is not removed. */ -long nonodes, endsite, outgrno, nextree, which; +long nonodes, endsite, nextree, which; boolean interleaved, printdata, outgropt, treeprint, dotdiff; steptr weight, category, alias, location, ally; sequence y, convtab; --- a/src/dnacomp.c +++ b/src/dnacomp.c @@ -53,8 +53,6 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; node *root, *p; long chars, col, ith, njumble, jumb, msets, numtrees; --- a/src/dnadist.c +++ b/src/dnadist.c @@ -27,7 +27,6 @@ Char infilename[FNMLNGTH], catfilename[FNMLNGTH], weightfilename[FNMLNGTH]; const char* outfilename; -AjPFile embossoutfile; long sites, categs, weightsum, datasets, ith, rcategs; boolean freqsfrom, jukes, kimura, logdet, gama, invar, similarity, lower, f84, --- a/src/dnainvar.c +++ b/src/dnainvar.c @@ -51,7 +51,6 @@ Char infilename[FNMLNGTH], weightfilename[FNMLNGTH]; const char* outfilename; -AjPFile embossoutfile; long sites, msets, ith; boolean weights, progress, prntpat, printinv, mulsets, firstset, justwts; --- a/src/dnaml.c +++ b/src/dnaml.c @@ -93,12 +93,10 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; double *rate, *rrate, *probcat; long nonodes2, sites, weightsum, categs, datasets, ith, njumble, jumb; -long parens, outgrno; +long parens; boolean freqsfrom, global, jumble, weights, trout, usertree, ctgry, rctgry, auto_, hypstate, ttr, progress, mulsets, justwts, firstset, improve, smoothit, polishing, lngths, gama, invar,inserting=false; --- a/src/dnamlk.c +++ b/src/dnamlk.c @@ -119,8 +119,6 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; double *rrate; long sites, weightsum, categs, datasets, ith, njumble, jumb, numtrees, shimotrees; /* sites = number of sites in actual sequences --- a/src/dnamove.c +++ b/src/dnamove.c @@ -127,7 +127,6 @@ node *root; const char* outtreename; -AjPFile embossouttree; long chars, screenlines, col, treelines, leftedge, topedge, vmargin, hscroll, vscroll, scrollinc, screenwidth, farthest, whichtree, othertree; --- a/src/dnapenny.c +++ b/src/dnapenny.c @@ -47,8 +47,6 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; node *root, *p; long *zeros=NULL; long chars, howmany, howoften, col, msets, ith; --- a/src/dollop.c +++ b/src/dollop.c @@ -10,7 +10,6 @@ #define maxtrees 100 /* maximum number of tied trees stored */ -AjPPhyloState* phylostates = NULL; AjPPhyloProp phyloanc = NULL; AjPPhyloProp phyloweights = NULL; AjPPhyloTree* phylotrees = NULL; @@ -47,8 +46,6 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; node *root; --- a/src/dolmove.c +++ b/src/dolmove.c @@ -11,7 +11,6 @@ #define overr 4 #define which 1 -AjPPhyloState* phylostates = NULL; AjPPhyloProp phyloanc = NULL; AjPPhyloProp phylofact = NULL; AjPPhyloProp phyloweights = NULL; @@ -73,10 +72,9 @@ Char infilename[FNMLNGTH],intreename[FNMLNGTH], ancfilename[FNMLNGTH], factfilename[FNMLNGTH], weightfilename[FNMLNGTH]; const char* outtreename; -AjPFile embossouttree; node *root; -long outgrno, col, screenlines, screenwidth, scrollinc,treelines, +long col, screenlines, screenwidth, scrollinc,treelines, leftedge,topedge,vmargin,hscroll,vscroll,farthest; /* outgrno indicates outgroup */ boolean weights, thresh, ancvar, questions, dollo, factors, --- a/src/dolpenny.c +++ b/src/dolpenny.c @@ -15,7 +15,6 @@ typedef double *valptr; typedef long *placeptr; -AjPPhyloState* phylostates = NULL; AjPPhyloProp phyloanc = NULL; AjPPhyloProp phyloweights = NULL; @@ -40,8 +39,6 @@ Char infilename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH]; const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; node *root; long howmany, howoften, col, msets, ith; --- a/src/draw.c +++ b/src/draw.c @@ -10,6 +10,20 @@ #include "phylip.h" #include "draw.h" +#ifndef X_DISPLAY_MISSING +Display *display; +int x, y; +unsigned int width, height; +char *fontrsc; +XFontStruct *fontst; +XGCValues gcv; +GC gc1; +XtAppContext appcontext; +Widget toplevel; +int nargc; +char** nargv; +#endif + #ifdef QUICKC struct videoconfig myscreen; void setupgraphics(); --- a/src/factor.c +++ b/src/factor.c @@ -54,7 +54,6 @@ const char* outfactname; const char* outancname; AjPFile inputfile; -AjPFile embossoutfile; AjPFile embossoutfact; AjPFile embossoutanc; --- a/src/fitch.c +++ b/src/fitch.c @@ -60,11 +60,9 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; Char infilename[FNMLNGTH], intreename[FNMLNGTH]; -long nonodes2, outgrno, nums, col, datasets, ith, njumble, jumb=0, numtrees; +long nonodes2, nums, col, datasets, ith, njumble, jumb=0, numtrees; long inseed; vector *x; intvector *reps; --- a/src/freqboot.c +++ b/src/freqboot.c @@ -52,7 +52,6 @@ const char* outfilename; -AjPFile embossoutfile; const char* outweightfilename; AjPFile embossoutweightfile; --- a/src/gendist.c +++ b/src/gendist.c @@ -24,7 +24,6 @@ #endif const char* outfilename; -AjPFile embossoutfile; long loci, totalleles, df, datasets, ith; long nonodes; --- a/src/kitsch.c +++ b/src/kitsch.c @@ -51,8 +51,6 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; Char infilename[FNMLNGTH], intreename[FNMLNGTH]; --- a/src/mix.c +++ b/src/mix.c @@ -13,7 +13,6 @@ typedef long *placeptr; -AjPPhyloState* phylostates = NULL; AjPPhyloProp phyloweights = NULL; AjPPhyloProp phyloanc = NULL; AjPPhyloProp phylomix = NULL; @@ -52,11 +51,9 @@ Char infilename[FNMLNGTH], intreename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH]; const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; node2 *root; -long outgrno, msets, ith, njumble, jumb, numtrees; +long msets, ith, njumble, jumb, numtrees; /* outgrno indicates outgroup */ long inseed, inseed0; boolean jumble, usertree, weights, ancvar, questions, allsokal, --- a/src/move.c +++ b/src/move.c @@ -13,7 +13,6 @@ #define which 1 -AjPPhyloState* phylostates = NULL; AjPPhyloProp phyloweights = NULL; AjPPhyloProp phyloanc = NULL; AjPPhyloProp phylomix = NULL; @@ -77,10 +76,9 @@ char infilename[FNMLNGTH],intreename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH], factfilename[FNMLNGTH]; const char* outtreename; -AjPFile embossouttree; node *root; -long outgrno, screenlines, col, treelines, leftedge, topedge, +long screenlines, col, treelines, leftedge, topedge, vmargin, hscroll, vscroll, scrollinc, screenwidth, farthest; /* outgrno indicates outgroup */ boolean weights, outgropt, ancvar, questions, allsokal, --- a/src/neighbor.c +++ b/src/neighbor.c @@ -32,11 +32,9 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; Char infilename[FNMLNGTH]; -long nonodes2, outgrno, col, datasets, ith; +long nonodes2, col, datasets, ith; long inseed; vector *x; intvector *reps; --- a/src/pars.c +++ b/src/pars.c @@ -9,7 +9,6 @@ #define MAXNUMTREES 1000000 /* bigger than number of user trees can be */ -AjPPhyloState* phylostates = NULL; AjPPhyloProp phyloweights = NULL; AjPPhyloTree* phylotrees = NULL; --- a/src/penny.c +++ b/src/penny.c @@ -12,7 +12,6 @@ #define often 100 /* how often to notify how many trees examined */ #define many 1000 /* how many multiples of howoften before stop */ -AjPPhyloState* phylostates = NULL; AjPPhyloProp phyloweights = NULL; AjPPhyloProp phyloanc = NULL; AjPPhyloProp phylomix = NULL; @@ -44,11 +43,9 @@ Char infilename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH]; const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; node2 *root; -long outgrno, rno, howmany, howoften, col, msets, ith; +long rno, howmany, howoften, col, msets, ith; /* outgrno indicates outgroup */ boolean weights, ancvar, questions, allsokal, allwagner, --- a/src/phylip.c +++ b/src/phylip.c @@ -46,7 +46,8 @@ AjPFile embossancfile; AjPFile embossmixfile; AjPFile embossfactfile; -long spp, words, bits; +AjPPhyloState* phylostates = NULL; +long spp, words, bits, outgrno; boolean ibmpc, ansi, tranvsp; naym *nayme; /* names of species */ --- a/src/proml.c +++ b/src/proml.c @@ -89,8 +89,6 @@ Char infilename[100], intreename[100], catfilename[100], weightfilename[100]; const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; double *rate, *rrate, *probcat; long nonodes2, sites, weightsum, categs, --- a/src/promlk.c +++ b/src/promlk.c @@ -88,8 +88,6 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; Char infilename[FNMLNGTH], intreename[FNMLNGTH], catfilename[FNMLNGTH], weightfilename[FNMLNGTH]; --- a/src/protdist.c +++ b/src/protdist.c @@ -79,7 +79,6 @@ char infilename[100], catfilename[100], weightfilename[100]; const char* outfilename; -AjPFile embossoutfile; /* Local variables for makedists, propagated globally for c version: */ --- a/src/protpars.c +++ b/src/protpars.c @@ -76,8 +76,6 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; node *root; long chars, col, msets, ith, njumble, jumb, numtrees; --- a/src/restboot.c +++ b/src/restboot.c @@ -54,7 +54,6 @@ const char* outfilename; -AjPFile embossoutfile; const char* outweightfilename; AjPFile embossoutweightfile; --- a/src/restdist.c +++ b/src/restdist.c @@ -13,7 +13,6 @@ extern sequence y; -AjPPhyloState* phylostates = NULL; #ifndef OLDC @@ -40,7 +39,6 @@ Char infilename[FNMLNGTH]; const char* outfilename; -AjPFile embossoutfile; long sites, weightsum, datasets, ith; boolean restsites, neili, gama, weights, lower, --- a/src/restml.c +++ b/src/restml.c @@ -17,7 +17,6 @@ AjPPhyloProp phyloweights = NULL; AjPPhyloTree* phylotrees; -AjPPhyloState* phylostates = NULL; #ifndef OLDC /* function prototypes */ @@ -101,8 +100,6 @@ const char* outfilename; const char* outtreename; -AjPFile embossoutfile; -AjPFile embossouttree; ajint numwts; --- a/src/retree.c +++ b/src/retree.c @@ -123,7 +123,7 @@ node *root, *garbage; -long nonodes, outgrno, screenwidth, vscreenwidth, +long nonodes, screenwidth, vscreenwidth, screenlines, col, treenumber, leftedge, topedge, treelines, hscroll, vscroll, scrollinc, whichtree, othertree, numtrees, treesread; @@ -145,7 +145,6 @@ char intreename[FNMLNGTH]; const char* outtreename; -AjPFile embossouttree; boolean subtree, written, readnext; node *nuroot; --- a/src/seqbootall.c +++ b/src/seqbootall.c @@ -109,7 +109,6 @@ const char* outfilename; -AjPFile embossoutfile; const char* outweightfilename; AjPFile embossoutweightfile; --- a/src/seqboot.c +++ b/src/seqboot.c @@ -92,7 +92,6 @@ const char* outfilename; -AjPFile embossoutfile; const char* outweightfilename; AjPFile embossoutweightfile; --- a/src/seq.c +++ b/src/seq.c @@ -7,7 +7,7 @@ Permission is granted to copy and use this program provided no fee is charged for it and provided that this copyright notice is not removed. */ -long nonodes, endsite, outgrno, nextree, which; +long nonodes, endsite, nextree, which; boolean interleaved, printdata, outgropt, treeprint, dotdiff, transvp; steptr weight, category, alias, location, ally; sequence y; --- a/src/treedist.c +++ b/src/treedist.c @@ -16,7 +16,6 @@ extern node *root; const char* outfilename; -AjPFile embossoutfile; long trees_in_1, trees_in_2; --- a/src/treedistpair.c +++ b/src/treedistpair.c @@ -16,7 +16,6 @@ extern node *root; const char* outfilename; -AjPFile embossoutfile; long trees_in_1, trees_in_2;