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gentoo-overlay/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-...

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--- 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;
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