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111 lines
3.1 KiB
111 lines
3.1 KiB
--- a/csrc/dnapars.c
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+++ b/csrc/dnapars.c
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@@ -77,41 +77,43 @@
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/* function prototypes */
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-Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
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+extern Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
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weightfilename[FNMLNGTH];
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char basechar[32]="ACMGRSVTWYHKDBNO???????????????";
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-node *root;
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-long chars, col, msets, ith, njumble, jumb, maxtrees;
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+extern node *root;
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+extern long chars, col, msets, ith, njumble, jumb;
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+long maxtrees;
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/* chars = number of sites in actual sequences */
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-long inseed, inseed0;
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-double threshold;
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-boolean jumble, usertree, thresh, weights, thorough, rearrfirst,
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- trout, progress, stepbox, ancseq, mulsets, justwts, firstset, mulf,
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- multf;
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+extern long inseed, inseed0;
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+extern double threshold;
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+boolean thorough, rearrfirst, mulf, multf;
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+extern boolean justwts, ancseq, weights, thresh, jumble, usertree, trout, mulsets, progress, stepbox, firstset;
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steptr oldweight;
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-longer seed;
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-pointarray treenode; /* pointers to all nodes in tree */
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-long *enterorder;
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+extern longer seed;
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+extern pointarray treenode; /* pointers to all nodes in tree */
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+extern long *enterorder;
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long *zeros;
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/* local variables for Pascal maketree, propagated globally for C version: */
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-long minwhich;
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+extern long minwhich;
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static double like, minsteps, bestyet, bestlike, bstlike2;
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-boolean lastrearr, recompute;
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-double nsteps[maxuser];
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-long **fsteps;
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-node *there, *oldnufork;
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-long *place;
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-bestelm *bestrees;
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-long *threshwt;
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+extern boolean lastrearr, recompute;
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+extern double nsteps[maxuser];
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+extern long **fsteps;
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+extern node *there;
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+node *oldnufork;
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+extern long *place;
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+extern bestelm *bestrees;
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+extern long *threshwt;
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baseptr nothing;
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-gbases *garbage;
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-node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
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+extern gbases *garbage;
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+extern node *temp, *temp1;
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+node *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
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*tmp2, *tmp3, *tmprm, *tmpadd;
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-boolean *names;
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+extern boolean *names;
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node *grbg;
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-char *progname;
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+extern char *progname;
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static void getoptions(int arg_maxtrees, dnapars_S_option s_option)
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--- a/csrc/phylip.c
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+++ b/csrc/phylip.c
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@@ -35,6 +35,8 @@
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#include "phylip.h"
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+boolean javarun;
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+
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#ifdef WIN32
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#include <windows.h>
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/* for console code (clear screen, text color settings) */
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--- a/csrc/phylip.h
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+++ b/csrc/phylip.h
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@@ -342,7 +342,7 @@
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/* Lower-triangular format. */
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#define MAT_LOWERTRI (MAT_LOWER | MAT_MACHINE)
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-boolean javarun;
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+extern boolean javarun;
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typedef long *steptr;
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typedef long longer[6];
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@@ -363,7 +363,6 @@
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extern boolean ibmpc, ansi, tranvsp;
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//extern naym *nayme; /* names of species */
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extern char* *nayme; /* names of species */
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-boolean firstplotblock; // for debugging BMP output
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#define ebcdic EBCDIC
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--- a/csrc/protpars.c
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+++ b/csrc/protpars.c
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@@ -127,7 +127,7 @@
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node *temp, *temp1;
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Char ch;
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aas tmpa;
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-char *progname;
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+extern char *progname;
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/* Local variables for maketree, propagated globally for c version: */
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long minwhich;
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