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