biology/mapm3: Reformat patches.
Make them compliant with the expected format.
This commit is contained in:
parent
f30b90774b
commit
0add9fcff9
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=547537
@ -1,5 +1,5 @@
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--- Makefile.orig 1993-02-10 07:12:59.000000000 +0100
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+++ Makefile 2014-01-12 18:47:03.605582463 +0100
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--- Makefile.orig 1993-02-10 06:12:59 UTC
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+++ Makefile
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@@ -16,6 +16,7 @@
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####
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#### For Macs with A/UX, use: SYS= -D_SYS_AUX
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@ -17,7 +17,7 @@
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#### Next define the system libraries to link with Mapmaker. On SunOS, Ultrix
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#### and other vanilla-ish BSD systems, the correct setting is:
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@@ -70,9 +71,11 @@
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@@ -70,9 +71,11 @@ DIR= /usr/local/bin
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#### (see the end of readline/readline.c). Readline will not compile on
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#### A/UX without using GCC instead of A/UX's cc (because it needs alloca).
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@ -32,7 +32,7 @@
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#### Now we specify the commands used to compile MAPMAKER. The stuff
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#### below works on Sun SPARCStations running SunOS 4.1.x (aka Solaris 1.x)
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@@ -82,8 +85,8 @@
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@@ -82,8 +85,8 @@ GNU_LIBS= -L$(RDLN) -lreadline
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#### person at your site should be able to figure out what to do almost
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#### trivially. See the file INSTALL.ME for details.
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@ -1,6 +1,6 @@
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--- lib/iolib.c.orig 2008-04-04 20:05:29.000000000 +0000
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+++ lib/iolib.c 2008-03-23 15:39:56.000000000 +0000
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@@ -299,7 +299,7 @@
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--- lib/iolib.c.orig 1993-02-09 16:35:24 UTC
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+++ lib/iolib.c
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@@ -299,7 +299,7 @@ int length;
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}
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@ -1,6 +1,6 @@
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--- lib/iolib.h.orig 2008-04-04 20:05:29.000000000 +0000
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+++ lib/iolib.h 2008-04-03 20:00:49.000000000 +0000
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@@ -53,9 +53,9 @@
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--- lib/iolib.h.orig 1993-02-09 16:35:27 UTC
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+++ lib/iolib.h
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@@ -53,9 +53,9 @@ sprintf() can spew out some very large strings of char
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conditions. Assume its really only one (or maybe 2-3) lines. ps_ is similar,
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but for internal use only by the functions in this library.
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@ -12,7 +12,7 @@
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However, the string space used to hold the input line is reused, and
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any pointers into the ln string which you saved may point to trash
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after one of these calls. Ln is alloced for 2K chars, leaving lots of
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@@ -66,7 +66,7 @@
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@@ -66,7 +66,7 @@ processing on the output string, including trying to w
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word breaks, converting tabs to spaces (every 8 chars), buffering
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output (perhaps multiple lines!) and more. The do_fwrite() function does
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not do this. Similarly, the getln() function despace()es,
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@ -21,7 +21,7 @@
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finput() functions do not [yes, it's a somewhat odd inconsistancy, but
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it's handy].
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@@ -254,6 +254,14 @@
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@@ -254,6 +254,14 @@ bool string_editor(); /* args: char *prompt, *str; int
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files! (The obvious exception is logging and input redirection, for which
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you should use the rather carefuly crafted routines described above!) */
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@ -36,7 +36,7 @@
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bool make_filename(); /* args: char *name; int mode; char *extension;
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This turns name into a perfectly valid file name, and returns TRUE if this
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was possible. The name may include a directory specification - otherwise it
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@@ -277,7 +285,7 @@
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@@ -277,7 +285,7 @@ FILE *open_file(); /* args: char *name, *mode; on fai
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#define APPEND "a"
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void close_file(); /* args: FILE *fp; */
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@ -45,7 +45,7 @@
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will be able to grab a new line from the file. */
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bool end_of_text(); /* args: FILE *fp; Like an end-of-file test, except it also
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returns TRUE if rest of the file is white. As a side-effect, it will step
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@@ -289,17 +297,17 @@
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@@ -289,17 +297,17 @@ void do_fwrite(); /* args: FILE *fp; char *string; no
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#define fpr(fp) fprint(fp,ps)
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#define fwp(fp) fwrite(fp,ps)
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@ -67,7 +67,7 @@
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beginning with a '#' in the leftmost position. Also, each time any line is
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read from the file (data, null, or comment), *count is incremented. */
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@@ -329,7 +337,7 @@
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@@ -329,7 +337,7 @@ extern int num_file_args, dos_output, prep_it, append_
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extern char *ps_, *ln_; /* input and output strings for the library only */
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extern char *linebuf; /* tty output buffer */
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@ -1,6 +1,6 @@
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--- lib/makehelp.c.orig 2008-04-04 20:05:29.000000000 +0000
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+++ lib/makehelp.c 2008-03-27 21:52:37.000000000 +0000
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@@ -131,7 +131,7 @@
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--- lib/makehelp.c.orig 1993-02-09 21:19:35 UTC
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+++ lib/makehelp.c
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@@ -131,7 +131,7 @@ char *name;
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{
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close_file(file);
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@ -9,7 +9,7 @@
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close_file(hlp);
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write_topics_and_end();
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@@ -172,9 +172,9 @@
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@@ -172,9 +172,9 @@ char *argv[];
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strcpy(man_name, argv[4]);
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strcpy(code_failed,code_name);
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@ -21,7 +21,7 @@
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FORCE_DIR,argv[5]);
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file= open_file(file_name,READ);
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@@ -187,16 +187,16 @@
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@@ -187,16 +187,16 @@ char *argv[];
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matrix(entry,MAX_COMMANDS,MAXLINE+1,char);
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/* start help file 12345678901234567890123456789012345 */
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@ -43,7 +43,7 @@
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/* man file */
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man_write_title();
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@@ -242,7 +242,7 @@
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@@ -242,7 +242,7 @@ char *argv[];
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strcpy(name,str+i); despace(name);
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nextstr();
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sf(ps,"\t%s... ",name); pr(); flush();
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@ -52,7 +52,7 @@
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if (streq(type,"cmd")) parse_entry(CMD,name,abbreviation);
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else if (streq(type,"opt")) parse_entry(OPT,name,abbreviation);
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else if (streq(type,"param")) parse_entry(PAR,name,abbreviation);
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@@ -419,7 +419,7 @@
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@@ -419,7 +419,7 @@ void write_topics_and_end()
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sf(ps," mktopic(%d,\"%s\",TOP,%ldl);\n",s,temp,position[s]);
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fpr(code); s++;
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}
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@ -61,7 +61,7 @@
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}
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@@ -681,7 +681,7 @@
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@@ -681,7 +681,7 @@ void man_write_contents()
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case TOP:
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man_write_line("");
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strcpy(upcase,section[s]); uppercase(upcase);
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@ -70,7 +70,7 @@
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case CMD:
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strcpy(upcase,entry[i]); uppercase(upcase);
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sf(temp," %s Command ",upcase); break;
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@@ -718,7 +718,7 @@
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@@ -718,7 +718,7 @@ void man_write_contents()
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if (entry_type[i]==TOP) {
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man_write_line("");
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strcpy(upcase,section[s]); uppercase(upcase);
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@ -1,6 +1,6 @@
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--- lib/shell.c.orig 2008-04-04 20:05:29.000000000 +0000
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+++ lib/shell.c 2008-03-27 21:24:20.000000000 +0000
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@@ -129,7 +129,7 @@
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--- lib/shell.c.orig 1993-02-09 16:35:25 UTC
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+++ lib/shell.c
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@@ -129,7 +129,7 @@ char *version_filename;
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run {
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strcpy(name,version_filename);
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@ -9,7 +9,7 @@
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FORCE_DIR,CODE_DIR)) send(CANTOPEN);
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fp=open_file(name,READ);
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finput(fp,ln_,MAXLINE); p=ln_; /* don't hack &ln_ */
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@@ -226,7 +226,7 @@
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@@ -226,7 +226,7 @@ char *program, *version, *copyright, *help_filename;
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help_uses_wimp_help= FALSE;
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help_file=NULL;
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@ -18,7 +18,7 @@
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DEFAULT_DIR,CODE_DIR)) {
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run help_file=open_file(help_filename,READ);
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except_when(CANTOPEN) {}
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@@ -950,7 +950,7 @@
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@@ -950,7 +950,7 @@ command run_from_file()
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use_uncrunched_args();
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get_one_arg(stoken,sREQUIRED,file_name);
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@ -27,7 +27,7 @@
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error("bad input file name");
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else redirect_input(file_name,TRUE); /* verbose -> messages */
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}
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@@ -972,7 +972,7 @@
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@@ -972,7 +972,7 @@ command do_photo()
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usage_error(1);
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} else if (!nullstr(file_name)) {
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@ -36,7 +36,7 @@
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sf(ps,"error: Bad photo file name");
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if (!photo_to_file(file_name,"a"))
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sf(ps,"error: Unable to open photo file '%s'\n",file_name);
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@@ -1080,12 +1080,12 @@
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@@ -1080,12 +1080,12 @@ command help()
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else if (topic_help_key[i]==HELPLESS) print(NO_HELP_KEY);
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else {
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fgoto_line(help_file,topic_help_key[i]);
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@ -51,7 +51,7 @@
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}
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if (!got_any) print(NO_HELP_KEY);
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}
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@@ -1131,12 +1131,12 @@
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@@ -1131,12 +1131,12 @@ command help()
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else if (cmd[i]->help_key==HELPLESS) print(NO_HELP_KEY);
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else {
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fgoto_line(help_file,cmd[i]->help_key);
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@ -66,7 +66,7 @@
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}
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if (!got_any) print(NO_HELP_KEY);
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}
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@@ -1164,10 +1164,10 @@
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@@ -1164,10 +1164,10 @@ command about()
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{ print(NO_HELP_KEY); nl(); print(SURROGATE_ABOUT); }
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else {
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fgoto_line(help_file,n);
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@ -1,6 +1,6 @@
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--- lib/syscode.c.orig 2008-04-04 20:05:29.000000000 +0000
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+++ lib/syscode.c 2008-03-27 21:03:12.000000000 +0000
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@@ -198,7 +198,7 @@
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--- lib/syscode.c.orig 1993-02-09 16:35:26 UTC
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+++ lib/syscode.c
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@@ -198,7 +198,7 @@ long index;
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long fseekvalue= 0L;
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frewind(fp);
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run while (fseekvalue < index-1) {
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@ -9,7 +9,7 @@
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fseekvalue+=len(ln)+1;
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} except_when(ENDOFILE) return(FALSE);
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return(TRUE);
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@@ -742,26 +742,26 @@
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@@ -742,26 +742,26 @@ char *argv[];
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} else if (matches(argv[i]+1,"load")) {
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check_file_arg(*argc_ptr-i,argv[i+1],file_arg[LOAD_FILE_ARG],
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@ -1,6 +1,6 @@
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--- lib/system.h.orig 2008-04-04 20:05:29.000000000 +0000
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+++ lib/system.h 2008-03-27 20:49:34.000000000 +0000
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@@ -43,6 +43,7 @@
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--- lib/system.h.orig 1993-02-09 16:35:28 UTC
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+++ lib/system.h
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@@ -43,6 +43,7 @@ code, we suggest you use the following flags:
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_SYS_OSF Specifics for OSF/1 for DEC Alpha (like, if it ever ships)
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_SYS_AIX Specifics for the inferior but marketable AIX (RISC or other?)
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_SYS_HPUX Specifics for HP-UX (8.x?) for HP 9000/700 series.
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@ -8,7 +8,7 @@
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_SYS_UNIX Basic Unix semantics, defined if any one of the above is
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_SYS_WATCOM Specifics for WATCOM C/386 9.0 with apropriate libraries
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@@ -86,6 +87,11 @@
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@@ -86,9 +87,14 @@ following and then #including "system.h":
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#else
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#ifdef _SYS_AUX
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#define _SYS_UNIX /* Note: NOT _SYS_MAC */
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@ -16,11 +16,14 @@
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+#ifdef _SYS_BSD
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+#define _SYS_UNIX
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+#else
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#endif
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#endif
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#endif
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+#endif
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#ifdef _SYS_WATCOM
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#define _SYS_DOS
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#endif
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#endif
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#endif
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@@ -191,6 +197,9 @@
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@@ -191,6 +197,9 @@ extern char *sys_errlist[]; extern int sys_nerr;
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#ifdef _SYS_ULTRIX
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#define SIGHANDLE void
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#endif
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@ -30,7 +33,7 @@
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@@ -210,10 +219,14 @@
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@@ -210,10 +219,14 @@ seem to be real portable, so be careful.
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#ifdef _SYS_ULTRIX
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#define USE_RANDOM
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#else
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@ -45,7 +48,7 @@
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/***************************** C-Library **************************************
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@@ -282,6 +295,14 @@
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@@ -282,6 +295,14 @@ Check out their usage (arguments, etc) in syscode.c to
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#define QSORT_LENGTH int /* actually width is an int, not a unsigned */
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#endif
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@ -60,7 +63,7 @@
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#ifdef _SYS_AUX /* just like ULTRIX? */
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#define CALLOC_PTR_TO char
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#define CALLOC_NUM_TYPE size_t /* unsigned in man page is wrong? */
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@@ -583,7 +604,7 @@
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@@ -583,7 +604,7 @@ robust and portable) interfaces are provided by the li
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#include <signal.h>
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#include <errno.h>
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#include <time.h> /* for ctime() def - Who does not have this file? */
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@ -1,6 +1,6 @@
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--- mapm/chroms.c.orig 2008-04-04 20:05:29.000000000 +0000
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+++ mapm/chroms.c 2008-03-27 21:25:42.000000000 +0000
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@@ -909,7 +909,7 @@
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--- mapm/chroms.c.orig 1993-02-09 16:35:02 UTC
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+++ mapm/chroms.c
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@@ -909,7 +909,7 @@ FILE *fp;
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write_map(fp, chromosome->map_list[i]);
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}
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@ -9,7 +9,7 @@
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for (locus=0; locus< raw.num_markers; locus++) {
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sf(ps,"*%-8s %2d",raw.locus_name[locus],assignment[locus]->status);
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fpr(fp);
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@@ -943,7 +943,7 @@
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@@ -943,7 +943,7 @@ FILE *fp;
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MAP *map;
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/* chromosomes */
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@ -18,7 +18,7 @@
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stoken(&ln,sREQUIRED,word);
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if (!streq(word,"*Chromosomes:") || !itoken(&ln,iREQUIRED,&num_chroms)) {
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baddata("error finding *Chromosomes:");
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@@ -957,7 +957,7 @@
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@@ -957,7 +957,7 @@ FILE *fp;
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baddata("listed number of chromosomes and actual number do not agree");
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}
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|
@ -1,6 +1,6 @@
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--- mapm/database.c.orig 2008-04-04 20:05:29.000000000 +0000
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+++ mapm/database.c 2008-03-27 21:26:48.000000000 +0000
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@@ -45,7 +45,7 @@
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--- mapm/database.c.orig 1993-02-09 16:35:02 UTC
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+++ mapm/database.c
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@@ -45,7 +45,7 @@ command import()
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get_one_arg(stoken, sREQUIRED, out_name);
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/* force file extension to be ".data" */
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|
@ -1,6 +1,6 @@
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--- mapm/info.c.orig 2008-04-04 20:05:29.000000000 +0000
|
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+++ mapm/info.c 2008-03-27 21:26:18.000000000 +0000
|
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@@ -966,9 +966,9 @@
|
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--- mapm/info.c.orig 1993-02-09 16:35:03 UTC
|
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+++ mapm/info.c
|
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@@ -966,9 +966,9 @@ FILE *fp;
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class[locus]);
|
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fpr(fp);
|
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}
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@ -12,7 +12,7 @@
|
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}
|
||||
|
||||
|
||||
@@ -980,12 +980,12 @@
|
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@@ -980,12 +980,12 @@ FILE *fp;
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real rate;
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char temp_locus_name[NAME_LEN+2], word[TOKLEN+1];
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@ -27,7 +27,7 @@
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|
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if (!nstoken(&ln,sREQUIRED,temp_locus_name,NAME_LEN+1) ||
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temp_locus_name[0]!='*' || len(temp_locus_name)<2)
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@@ -1007,9 +1007,9 @@
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@@ -1007,9 +1007,9 @@ FILE *fp;
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order_next[locus]= ord_next;
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class[locus]= class_num;
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}
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|
@ -1,6 +1,6 @@
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--- mapm/map_info.h.orig 2008-04-04 20:05:29.000000000 +0000
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+++ mapm/map_info.h 2008-03-31 00:14:48.000000000 +0000
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@@ -215,7 +215,7 @@
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--- mapm/map_info.h.orig 1993-02-09 16:35:06 UTC
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+++ mapm/map_info.h
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@@ -215,7 +215,7 @@ typedef struct { /* working data for place cmd and ex
|
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/***** Chromosome framework, assignment, and placement stuff - chroms.c *****/
|
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|
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extern SAVED_LIST *chromosome; /* malloced by allocate_mapping_structs() */
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|
@ -1,5 +1,5 @@
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--- mapm/mapm.h.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ mapm/mapm.h 2008-03-16 13:53:32.000000000 +0000
|
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--- mapm/mapm.h.orig 1993-02-09 16:35:06 UTC
|
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+++ mapm/mapm.h
|
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@@ -19,7 +19,7 @@
|
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#define command void /* needed if INC_SHELL was not defined */
|
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#endif
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|
@ -1,6 +1,6 @@
|
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--- mapm/maps.c.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ mapm/maps.c 2008-03-23 15:39:56.000000000 +0000
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@@ -592,7 +592,7 @@
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--- mapm/maps.c.orig 1993-02-09 16:35:03 UTC
|
||||
+++ mapm/maps.c
|
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@@ -592,7 +592,7 @@ MAP *map;
|
||||
|
||||
clean_map(map);
|
||||
|
||||
@ -9,7 +9,7 @@
|
||||
if (!nstoken(&ln,sREQUIRED,name,NAME_LEN+1) || name[0]!='*' ||
|
||||
sscanf(ln,"%d %d %d %d %lf",&num_loci,&unlink,&sex,&errors,&like)!=5)
|
||||
baddata("expected *chrom-name # # # #");
|
||||
@@ -603,31 +603,31 @@
|
||||
@@ -603,31 +603,31 @@ MAP *map;
|
||||
strcpy(map->map_name,name+1); map->allow_errors= errors;
|
||||
map->num_loci=num_loci; map->log_like=like;
|
||||
|
||||
@ -49,7 +49,7 @@
|
||||
if (!itoken(&ln,iREQUIRED,&num)) send(CRASH);
|
||||
map->fix_interval[i]=num;
|
||||
}
|
||||
@@ -637,7 +637,7 @@
|
||||
@@ -637,7 +637,7 @@ MAP *map;
|
||||
matrix(map->error_lod,map->max_loci,raw.data.f2.num_indivs,real);
|
||||
}
|
||||
for (i=0; i<map->num_loci; i++) {
|
||||
@ -58,7 +58,7 @@
|
||||
if (!stoken(&ln,sREQUIRED,str) || !streq(str,"errors"))
|
||||
send(CRASH);
|
||||
if (!rtoken(&ln,rREQUIRED,&rnum)) send(CRASH);
|
||||
@@ -646,9 +646,9 @@
|
||||
@@ -646,9 +646,9 @@ MAP *map;
|
||||
for(j=0; j<raw.data.f2.num_indivs; j++)
|
||||
map->error_lod[i][j]= 0.0;
|
||||
} else {
|
||||
|
@ -1,6 +1,6 @@
|
||||
--- mapm/npt_cmds.c.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ mapm/npt_cmds.c 2008-03-27 21:27:12.000000000 +0000
|
||||
@@ -78,7 +78,7 @@
|
||||
--- mapm/npt_cmds.c.orig 1993-02-09 16:35:04 UTC
|
||||
+++ mapm/npt_cmds.c
|
||||
@@ -78,7 +78,7 @@ command draw_map()
|
||||
nomore_args(num_args);
|
||||
|
||||
run {
|
||||
|
@ -1,6 +1,6 @@
|
||||
--- mapm/print.c.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ mapm/print.c 2008-03-27 21:34:40.000000000 +0000
|
||||
@@ -540,7 +540,7 @@
|
||||
--- mapm/print.c.orig 1993-02-09 16:35:04 UTC
|
||||
+++ mapm/print.c
|
||||
@@ -540,7 +540,7 @@ bool haplo;
|
||||
}
|
||||
}
|
||||
|
||||
|
@ -1,6 +1,6 @@
|
||||
--- mapm/reader.c.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ mapm/reader.c 2008-03-27 21:10:18.000000000 +0000
|
||||
@@ -81,7 +81,7 @@
|
||||
--- mapm/reader.c.orig 1993-02-09 16:35:05 UTC
|
||||
+++ mapm/reader.c
|
||||
@@ -81,7 +81,7 @@ void data_init()
|
||||
|
||||
void getdataln(fp) /* get next nonblank,noncomment data file line */
|
||||
FILE *fp;
|
||||
@ -9,7 +9,7 @@
|
||||
|
||||
|
||||
void baddata(reason) /* send data reading error message */
|
||||
@@ -135,7 +135,7 @@
|
||||
@@ -135,7 +135,7 @@ bool *exists;
|
||||
char tmpname[PATH_LENGTH+1];
|
||||
|
||||
make_filename(name,FORCE_EXTENSION,ext);
|
||||
@ -18,7 +18,7 @@
|
||||
|
||||
fp=NULL; *exists=FALSE;
|
||||
run {
|
||||
@@ -162,7 +162,7 @@
|
||||
@@ -162,7 +162,7 @@ char *name, *oldext;
|
||||
bool exists;
|
||||
{
|
||||
char tmpname[PATH_LENGTH+1], oldname[PATH_LENGTH+1];
|
||||
@ -27,7 +27,7 @@
|
||||
strcpy(oldname,name); make_filename(oldname,FORCE_EXTENSION,oldext);
|
||||
|
||||
if (exists) { rename_file(name,oldname); }
|
||||
@@ -214,7 +214,7 @@
|
||||
@@ -214,7 +214,7 @@ bool israw;
|
||||
raw.data.f2.cross_type);
|
||||
print(" ok\n");
|
||||
|
||||
@ -36,7 +36,7 @@
|
||||
run {
|
||||
fp2=NULL;
|
||||
fp2=open_file(name,READ);
|
||||
@@ -228,7 +228,7 @@
|
||||
@@ -228,7 +228,7 @@ bool israw;
|
||||
close_file(fp2);
|
||||
} except_when(CANTOPEN) { } /* need a better handler */
|
||||
|
||||
@ -45,7 +45,7 @@
|
||||
run {
|
||||
fp2=NULL;
|
||||
fp2=open_file(name,READ);
|
||||
@@ -240,7 +240,7 @@
|
||||
@@ -240,7 +240,7 @@ bool israw;
|
||||
close_file(fp2);
|
||||
} except_when(CANTOPEN) { } /* need a better handler */
|
||||
|
||||
@ -54,7 +54,7 @@
|
||||
run {
|
||||
fp2=NULL;
|
||||
fp2=open_file(name,READ);
|
||||
@@ -285,39 +285,39 @@
|
||||
@@ -285,39 +285,39 @@ bool save_genos_too;
|
||||
run {
|
||||
strcpy(name,base_name);
|
||||
if (save_genos_too) {
|
||||
@ -104,7 +104,7 @@
|
||||
free_traits();
|
||||
}
|
||||
two_pt_touched= FALSE;
|
||||
@@ -576,15 +576,15 @@
|
||||
@@ -576,15 +576,15 @@ FILE *fp;
|
||||
char header[MAXLINE+1];
|
||||
|
||||
if (raw.data.f2.cross_type==F2_INTERCROSS)
|
||||
@ -125,7 +125,7 @@
|
||||
|
||||
sf(header,"%d %d %d\n",raw.filenumber,raw.data.f2.num_indivs,
|
||||
raw.num_markers); fprint(fp,header);
|
||||
@@ -593,7 +593,7 @@
|
||||
@@ -593,7 +593,7 @@ FILE *fp;
|
||||
sf(ps,"*%-10s ", raw.locus_name[i]);
|
||||
fpr(fp);
|
||||
for (j=0; j<raw.data.f2.num_indivs; j++) {
|
||||
@ -134,7 +134,7 @@
|
||||
sf(ps,"%c",raw.data.f2.allele[i][j]);
|
||||
fpr(fp);
|
||||
}
|
||||
@@ -828,9 +828,7 @@
|
||||
@@ -828,9 +828,7 @@ int chr;
|
||||
char *symb;
|
||||
{
|
||||
/* CHANGED FOR THIS VERION - NOW READS "-AHBCD" */
|
||||
@ -145,7 +145,7 @@
|
||||
else if (chr==symb[2]) return(HYBRID_TYPE_H);
|
||||
else if (chr==symb[3]) return(PARENTAL_TYPE_B);
|
||||
else if (chr==symb[4]) return(TYPE_NOT_A);
|
||||
@@ -856,26 +854,26 @@
|
||||
@@ -856,26 +854,26 @@ FILE *fp;
|
||||
fnl(fp);
|
||||
}
|
||||
fnl(fp);
|
||||
|
@ -1,6 +1,6 @@
|
||||
--- mapm/state.c.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ mapm/state.c 2008-04-03 19:37:40.000000000 +0000
|
||||
@@ -734,7 +734,7 @@
|
||||
--- mapm/state.c.orig 1993-02-09 16:35:05 UTC
|
||||
+++ mapm/state.c
|
||||
@@ -734,7 +734,7 @@ FILE *fp;
|
||||
{
|
||||
int i, usenum;
|
||||
|
||||
@ -9,7 +9,7 @@
|
||||
|
||||
sf(ps,"*PrintNames: %d\n",print_names); fpr(fp);
|
||||
sf(ps,"*Tolerance: %lf\n",tolerance); fpr(fp);
|
||||
@@ -852,5 +852,5 @@
|
||||
@@ -852,5 +852,5 @@ FILE *fp;
|
||||
load_table(context[i]->sequence_history,fp,INDEX_BY_NUMBER,num);
|
||||
}
|
||||
|
||||
|
@ -1,6 +1,6 @@
|
||||
--- mapm/sys_cmds.c.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ mapm/sys_cmds.c 2008-03-27 21:28:05.000000000 +0000
|
||||
@@ -98,7 +98,7 @@
|
||||
--- mapm/sys_cmds.c.orig 1993-02-09 16:35:06 UTC
|
||||
+++ mapm/sys_cmds.c
|
||||
@@ -98,7 +98,7 @@ bool prev_data, raw;
|
||||
close_file(fp);
|
||||
if (raw) {
|
||||
strcpy(run_file,name);
|
||||
@ -9,7 +9,7 @@
|
||||
if (!redirect_input(run_file,FALSE)) {
|
||||
sf(ps,"unable to run file '%s'... skipping initialization\n",
|
||||
run_file); pr();
|
||||
@@ -145,7 +145,7 @@
|
||||
@@ -145,7 +145,7 @@ command new_load_data()
|
||||
if (!prev_data) print("no data are loaded\n");
|
||||
else { sf(ps,DATA_LOADED,raw.filename,data_info(TRUE)); pr(); }
|
||||
} else {
|
||||
@ -18,7 +18,7 @@
|
||||
if (prev_data) try_to_unload(fp,TRUE,auto_save,TRUE,just_prepared);
|
||||
try_to_load(fp,name,prev_data,FALSE);
|
||||
just_prepared=FALSE;
|
||||
@@ -169,7 +169,7 @@
|
||||
@@ -169,7 +169,7 @@ command new_prepare()
|
||||
if (streq(&name[end-4],DATA_EXT) || streq(&name[end-4],DATA_OLD) ||...
|
||||
error(RAW_EXTENSION); */
|
||||
|
||||
@ -27,7 +27,7 @@
|
||||
if (prev_data) try_to_unload(fp,TRUE,auto_save,TRUE,just_prepared);
|
||||
try_to_load(fp,name,prev_data,TRUE);
|
||||
just_prepared=TRUE;
|
||||
@@ -186,7 +186,7 @@
|
||||
@@ -186,7 +186,7 @@ command new_save_data()
|
||||
get_one_arg(stoken,"",name); new_name= !nullstr(name);
|
||||
/* want to change this so it sets raw.filename only AFTER it writes OK */
|
||||
|
||||
@ -36,7 +36,7 @@
|
||||
{ sf(ps,BAD_FILENAME,name); error(ps); }
|
||||
|
||||
run {
|
||||
@@ -621,7 +621,7 @@
|
||||
@@ -621,7 +621,7 @@ command new_insert()
|
||||
for (j=num_seq_tokens-1; j>i; j--)
|
||||
strcpy(seq_tokens[j+1],seq_tokens[j]);
|
||||
/* this is severly broken, if len(appendage) > TOKLEN */
|
||||
|
@ -1,6 +1,6 @@
|
||||
--- mapm/two_cmds.c.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ mapm/two_cmds.c 2008-04-03 19:58:42.000000000 +0000
|
||||
@@ -698,11 +698,11 @@
|
||||
--- mapm/two_cmds.c.orig 1993-02-09 16:35:06 UTC
|
||||
+++ mapm/two_cmds.c
|
||||
@@ -698,11 +698,11 @@ command three_point()
|
||||
|
||||
if (!print_names) {
|
||||
print("\n log-likelihood differences\n");
|
||||
|
@ -1,6 +1,6 @@
|
||||
--- quant/qcmds.c.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ quant/qcmds.c 2008-03-27 21:30:08.000000000 +0000
|
||||
@@ -1348,7 +1348,7 @@
|
||||
--- quant/qcmds.c.orig 1993-02-09 21:12:33 UTC
|
||||
+++ quant/qcmds.c
|
||||
@@ -1348,7 +1348,7 @@ command load_data()
|
||||
if (nullstr(args)) {
|
||||
if (!data_loaded()) print(NO_LOADED_DATA); else {
|
||||
strcpy(tfile,raw.file);
|
||||
@ -9,7 +9,7 @@
|
||||
sf(ps,LOADED_DATA,raw.file,tfile,"",raw.n_indivs,
|
||||
(raw.data_type==BACKCROSS ? "backcross":"intercross"),
|
||||
raw.n_loci,raw.n_traits,maybe_s(raw.n_traits)); pr();
|
||||
@@ -1363,9 +1363,9 @@
|
||||
@@ -1363,9 +1363,9 @@ command load_data()
|
||||
nstoken(&args,sREQUIRED,dfile,PATH_LENGTH); tfile[0]='\0';
|
||||
nomore_args(num_args);
|
||||
run {
|
||||
@ -21,7 +21,7 @@
|
||||
|
||||
if (streq(ln,"prepared data f2 backcross")) {
|
||||
strcpy(geno_chars,default_backcross_chars);
|
||||
@@ -1384,11 +1384,11 @@
|
||||
@@ -1384,11 +1384,11 @@ command load_data()
|
||||
}
|
||||
|
||||
strcpy(tfile,dfile);
|
||||
@ -35,7 +35,7 @@
|
||||
send(CANTOPEN);
|
||||
fpc = open_file(mfile,READ);
|
||||
|
||||
@@ -1449,7 +1449,7 @@
|
||||
@@ -1449,7 +1449,7 @@ command prep_data()
|
||||
|
||||
out_name = get_temp_string();
|
||||
strcpy(out_name,in_name);
|
||||
@ -44,7 +44,7 @@
|
||||
|
||||
fp = open_file(in_name,READ);
|
||||
getdataln(fp); crunch(ln);
|
||||
@@ -1488,7 +1488,7 @@
|
||||
@@ -1488,7 +1488,7 @@ command save_status()
|
||||
name = mkstrcpy(raw.file);
|
||||
name3 = mkstrcpy(raw.file);
|
||||
name2 = "dummy.qtls";
|
||||
@ -53,7 +53,7 @@
|
||||
|
||||
/* The following accounts for the case where there is no file 'name'
|
||||
(i.e. it makes one) */
|
||||
@@ -1500,7 +1500,7 @@
|
||||
@@ -1500,7 +1500,7 @@ command save_status()
|
||||
close_file(fp);
|
||||
}
|
||||
|
||||
@ -62,7 +62,7 @@
|
||||
run {
|
||||
fp = open_file(name2, WRITE);
|
||||
sf(ps,"Now saving %s...\n",name); pr();
|
||||
@@ -1520,8 +1520,8 @@
|
||||
@@ -1520,8 +1520,8 @@ command save_status()
|
||||
}
|
||||
|
||||
name2="dummy.traits";
|
||||
@ -73,7 +73,7 @@
|
||||
run {
|
||||
fp = open_file(name2, WRITE);
|
||||
sf(ps,"Now saving %s...\n",name); pr();
|
||||
@@ -1560,7 +1560,7 @@
|
||||
@@ -1560,7 +1560,7 @@ FILE *fp;
|
||||
save_wiggle(fp,i);
|
||||
}
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
|
||||
fprintf(fp,"%d %d\n",num_compares,first_compare);
|
||||
for(i = 0; i < num_compares; i++) {
|
||||
@@ -1587,7 +1587,7 @@
|
||||
@@ -1587,7 +1587,7 @@ void load_qtl_files()
|
||||
|
||||
run {
|
||||
strcpy(name,raw.file);
|
||||
|
@ -1,6 +1,6 @@
|
||||
--- quant/qraw.c.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ quant/qraw.c 2008-03-27 21:30:39.000000000 +0000
|
||||
@@ -124,7 +124,7 @@
|
||||
--- quant/qraw.c.orig 1993-02-09 16:35:59 UTC
|
||||
+++ quant/qraw.c
|
||||
@@ -124,7 +124,7 @@ int data_loaded() { return(raw.file[0]!='\0'); }
|
||||
|
||||
void getdataln(fp) /* get next nonblank/noncomment data file line */
|
||||
FILE *fp;
|
||||
@ -9,7 +9,7 @@
|
||||
BADDATA_ln= ln; }
|
||||
real read_map_distance();
|
||||
void read_map_locus();
|
||||
@@ -426,13 +426,13 @@
|
||||
@@ -426,13 +426,13 @@ FILE *fp;
|
||||
|
||||
for(j=0;j<raw.n_indivs;j++) {
|
||||
if(j % 5 == 0 && j != 0)
|
||||
@ -25,7 +25,7 @@
|
||||
sf(ps,"*Print mapm loci: %d\n", print_mapm_loci);fpr(fp);
|
||||
sf(ps,"*Like tolerance: %lf\n",like_tolerance);fpr(fp);
|
||||
sf(ps,"*Brute force: %d\n",brute_force);fpr(fp);
|
||||
@@ -452,21 +452,21 @@
|
||||
@@ -452,21 +452,21 @@ FILE *fp;
|
||||
sf(ps, "chr%d %d\n", i+1, raw.chrom_n_loci[i]); fpr(fp);
|
||||
for(j=0;j<raw.chrom_n_loci[i];j++) {
|
||||
if(j % 18 == 0 && j != 0)
|
||||
|
@ -1,6 +1,6 @@
|
||||
--- sun/xmapmaker.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ sun/xmapmaker 2008-04-04 19:59:32.000000000 +0000
|
||||
@@ -10,5 +10,5 @@
|
||||
--- sun/xmapmaker.orig 1993-02-10 05:57:29 UTC
|
||||
+++ sun/xmapmaker
|
||||
@@ -10,5 +10,5 @@ if (-e /usr/openwin/bin/xterm) then
|
||||
else if (-e /usr/openwin/demo/xterm) then
|
||||
exec /usr/openwin/demo/xterm $xoptions $fontsize -e $program $*
|
||||
else
|
||||
|
@ -1,6 +1,6 @@
|
||||
--- sun/xqtl.orig 2008-04-04 20:05:29.000000000 +0000
|
||||
+++ sun/xqtl 2008-04-04 19:59:41.000000000 +0000
|
||||
@@ -10,5 +10,5 @@
|
||||
--- sun/xqtl.orig 1993-02-10 05:57:29 UTC
|
||||
+++ sun/xqtl
|
||||
@@ -10,5 +10,5 @@ if (-e /usr/openwin/bin/xterm) then
|
||||
else if (-e /usr/openwin/demo/xterm) then
|
||||
exec /usr/openwin/demo/xterm $xoptions $fontsize -e $program $*
|
||||
else
|
||||
|
Loading…
Reference in New Issue
Block a user