From 97d4b58c284fc7d37063ca87fd02493b551abe31 Mon Sep 17 00:00:00 2001 From: Christian Weisgerber Date: Sat, 15 Feb 2003 18:43:14 +0000 Subject: [PATCH] Update to 1.83. PR: 48264 Submitted by: David A. Bader --- biology/clustalw/Makefile | 4 +- biology/clustalw/distinfo | 2 +- biology/clustalw/files/patch-aa | 6 +- biology/clustalw/files/patch-ab | 15 +++- biology/clustalw/files/patch-ac | 132 +++++++++++++++++++++++++++++++- biology/clustalw/files/patch-ae | 32 ++++---- biology/clustalw/files/patch-af | 6 +- biology/clustalw/files/patch-ag | 128 ------------------------------- biology/clustalw/files/patch-ah | 6 +- biology/clustalw/files/patch-ai | 6 +- biology/clustalw/files/patch-aj | 13 ++-- biology/clustalw/files/patch-ak | 10 --- biology/clustalw/pkg-comment | 1 - 13 files changed, 179 insertions(+), 182 deletions(-) delete mode 100644 biology/clustalw/files/patch-ag delete mode 100644 biology/clustalw/files/patch-ak delete mode 100644 biology/clustalw/pkg-comment diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile index ffd6ce7e1be4..920c77e970b8 100644 --- a/biology/clustalw/Makefile +++ b/biology/clustalw/Makefile @@ -6,13 +6,13 @@ # PORTNAME= clustalw -PORTVERSION= 1.82 -PORTREVISION= 2 +PORTVERSION= 1.83 CATEGORIES= biology MASTER_SITES= ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ DISTNAME= ${PORTNAME}${PORTVERSION}.UNIX MAINTAINER= dbader@eece.unm.edu +COMMENT= CLUSTAL W Multiple Sequence Alignment Program WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION} diff --git a/biology/clustalw/distinfo b/biology/clustalw/distinfo index 4a5de2b1cc1a..a67b9478f845 100644 --- a/biology/clustalw/distinfo +++ b/biology/clustalw/distinfo @@ -1 +1 @@ -MD5 (clustalw1.82.UNIX.tar.gz) = 8171ec890182383000bdb83de3022ca2 +MD5 (clustalw1.83.UNIX.tar.gz) = dc240277e5bb14ffc106d4a5fda87752 diff --git a/biology/clustalw/files/patch-aa b/biology/clustalw/files/patch-aa index 56e36ffce6ba..e3f7f4a8a915 100644 --- a/biology/clustalw/files/patch-aa +++ b/biology/clustalw/files/patch-aa @@ -1,6 +1,6 @@ ---- clustalw.c-orig Wed Jun 7 01:50:05 2000 -+++ clustalw.c Thu Jul 6 20:19:31 2000 -@@ -33,7 +33,7 @@ +--- clustalw.c.orig Thu Feb 13 15:17:15 2003 ++++ clustalw.c Thu Feb 13 14:50:51 2003 +@@ -34,7 +34,7 @@ #ifdef MSDOS char *help_file_name = "clustalw.hlp"; #else diff --git a/biology/clustalw/files/patch-ab b/biology/clustalw/files/patch-ab index 03e9eccaae85..110e16238cd1 100644 --- a/biology/clustalw/files/patch-ab +++ b/biology/clustalw/files/patch-ab @@ -1,6 +1,15 @@ ---- makefile.orig Wed Jun 7 16:55:06 2000 -+++ makefile Tue Aug 8 02:30:53 2000 -@@ -10,9 +10,9 @@ +--- makefile.orig Thu Feb 13 15:17:25 2003 ++++ makefile Thu Feb 13 15:15:48 2003 +@@ -4,15 +4,15 @@ + rm *.o + + OBJECTS = interface.o sequence.o showpair.o malign.o \ +- util.o trees.o gcgcheck.o prfalign.o pairalign.o \ +- calcgapcoeff.o calcprf1.o calcprf2.o calctree.o \ +- readmat.o alnscore.o random.o ++ util.o trees.o gcgcheck.o prfalign.o pairalign.o \ ++ calcgapcoeff.o calcprf1.o calcprf2.o calctree.o \ ++ readmat.o alnscore.o random.o HEADERS = general.h clustalw.h diff --git a/biology/clustalw/files/patch-ac b/biology/clustalw/files/patch-ac index fc4431f3b68f..57656a482e8b 100644 --- a/biology/clustalw/files/patch-ac +++ b/biology/clustalw/files/patch-ac @@ -1,6 +1,6 @@ ---- interface.c.orig Wed Jun 7 16:50:07 2000 -+++ interface.c Tue Aug 8 03:11:33 2000 -@@ -1078,7 +1078,7 @@ +--- interface.c.orig Thu Feb 13 15:17:33 2003 ++++ interface.c Thu Feb 13 15:26:28 2003 +@@ -1132,7 +1132,7 @@ /* added for File System Standards - Francois */ path1=(char *)ckalloc((strlen(path)+64)*sizeof(char)); strcpy(path1,path); @@ -9,3 +9,129 @@ lf=(sint)strlen(fname); deb=path1; +@@ -1224,7 +1224,7 @@ + if(strstr(temp, help_marker)){ + if(usemenu) { + fprintf(stdout,"\n"); +- getstr("Press [RETURN] to continue",lin2); ++ getstr("Press [RETURN] to continue",lin2,MAXLINE); + } + fclose(help_file); + return; +@@ -1236,7 +1236,7 @@ + if(usemenu) { + if(nlines >= PAGE_LEN) { + fprintf(stdout,"\n"); +- getstr("Press [RETURN] to continue or X to stop",lin2); ++ getstr("Press [RETURN] to continue or X to stop",lin2,MAXLINE); + if(toupper(*lin2) == 'X') { + fclose(help_file); + return; +@@ -1248,7 +1248,7 @@ + } + if(usemenu) { + fprintf(stdout,"\n"); +- getstr("Press [RETURN] to continue",lin2); ++ getstr("Press [RETURN] to continue",lin2,MAXLINE); + } + fclose(help_file); + } +@@ -1287,7 +1287,7 @@ + ++nlines; + if(nlines >= PAGE_LEN) { + fprintf(stdout,"\n"); +- getstr("Press [RETURN] to continue or X to stop",lin2); ++ getstr("Press [RETURN] to continue or X to stop",lin2,MAXLINE); + if(toupper(*lin2) == 'X') { + fclose(file); + return; +@@ -1298,7 +1298,7 @@ + } + fclose(file); + fprintf(stdout,"\n"); +- getstr("Press [RETURN] to continue",lin2); ++ getstr("Press [RETURN] to continue",lin2,MAXLINE); + } + + +@@ -1747,7 +1747,7 @@ + FILE *infile; + + if(usemenu) +- getstr("Enter name of the matrix file",lin2); ++ getstr("Enter name of the matrix file",lin2,MAXLINE); + else + strcpy(lin2,str); + +@@ -1773,7 +1773,7 @@ + FILE *infile; + + if(usemenu) +- getstr("Enter name of the matrix file",lin2); ++ getstr("Enter name of the matrix file",lin2,MAXLINE); + else + strcpy(lin2,str); + +@@ -2176,7 +2176,7 @@ + strcpy(local_prompt,"\n\nEnter new name to avoid overwriting "); + strcat(local_prompt," [%s]: "); + fprintf(stdout,local_prompt,file_name); +- gets(temp); ++ fgets(temp,FILENAMELEN+1,stdin); + if(*temp != EOS) strcpy(file_name,temp); + } + } +@@ -2184,7 +2184,7 @@ + strcpy(local_prompt,prompt); + strcat(local_prompt," [%s]: "); + fprintf(stdout,local_prompt,file_name); +- gets(temp); ++ fgets(temp,FILENAMELEN+1,stdin); + if(*temp != EOS) strcpy(file_name,temp); + } + +@@ -2385,7 +2385,7 @@ + if (usemenu) + fprintf(stdout,"\nUse the existing GUIDE TREE file, %s (y/n) ? [y]: ", + tree_name); +- gets(temp); ++ fgets(temp,MAXLINE,stdin); + if(*temp != 'n' && *temp != 'N') { + strcpy(phylip_name,tree_name); + use_tree = TRUE; +@@ -2617,7 +2617,7 @@ + + fprintf(stdout,"\nEnter a name for the guide tree file [%s]: ", + phylip_name); +- gets(temp); ++ fgets(temp,MAXLINE,stdin); + if(*temp != EOS) + strcpy(phylip_name,temp); + } +@@ -2719,7 +2719,7 @@ + #endif + fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 1, %s (y/n) ? [y]: ", + tree_name); +- gets(temp); ++ fgets(temp,MAXLINE,stdin); + if(*temp != 'n' && *temp != 'N') { + strcpy(p1_tree_name,tree_name); + use_tree1 = TRUE; +@@ -2745,7 +2745,7 @@ + #endif + fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 2, %s (y/n) ? [y]: ", + tree_name); +- gets(temp); ++ fgets(temp,MAXLINE,stdin); + if(*temp != 'n' && *temp != 'N') { + strcpy(p2_tree_name,tree_name); + use_tree2 = TRUE; +@@ -4203,7 +4203,7 @@ + if(usemenu) { + fprintf(stdout,"\nEnter a name for the parameter output file [%s]: ", + parname); +- gets(temp); ++ fgets(temp,FILENAMELEN+1,stdin); + if(*temp != EOS) + strcpy(parname,temp); + } diff --git a/biology/clustalw/files/patch-ae b/biology/clustalw/files/patch-ae index b9e3678ea31b..c1a976a1eb26 100644 --- a/biology/clustalw/files/patch-ae +++ b/biology/clustalw/files/patch-ae @@ -1,5 +1,5 @@ ---- amenu.c-orig Tue Feb 6 03:15:01 2001 -+++ amenu.c Thu Mar 21 10:19:02 2002 +--- amenu.c.orig Thu Feb 13 15:19:00 2003 ++++ amenu.c Thu Feb 13 15:21:10 2003 @@ -13,7 +13,8 @@ static jmp_buf jmpbuf; #ifndef VMS @@ -10,7 +10,7 @@ #endif #endif -@@ -176,7 +177,7 @@ +@@ -184,7 +185,7 @@ fprintf(stdout," H. HELP\n"); fprintf(stdout," X. EXIT (leave program)\n\n\n"); @@ -19,7 +19,7 @@ switch(toupper(*lin1)) { case '1': seq_input(FALSE); -@@ -260,7 +261,7 @@ +@@ -268,7 +269,7 @@ fprintf(stdout," H. HELP\n"); fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); @@ -28,7 +28,7 @@ if(*lin1 == EOS) return; switch(toupper(*lin1)) -@@ -353,7 +354,7 @@ +@@ -361,7 +362,7 @@ fprintf(stdout," H. HELP\n"); fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); @@ -37,7 +37,7 @@ if(*lin1 == EOS) return; switch(toupper(*lin1)) -@@ -449,7 +450,7 @@ +@@ -457,7 +458,7 @@ fprintf(stdout,"\n\n"); fprintf(stdout," H. HELP\n\n\n"); @@ -46,7 +46,7 @@ if( *lin2 == EOS) { return; } -@@ -525,7 +526,7 @@ +@@ -533,7 +534,7 @@ fprintf(stdout,"--\n"); @@ -55,7 +55,7 @@ if(*lin2 == EOS) return(output_struct_penalties); switch(toupper(*lin2)) -@@ -594,7 +595,7 @@ +@@ -602,7 +603,7 @@ fprintf(stdout," H. HELP\n"); fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); @@ -64,7 +64,7 @@ if(*lin1 == EOS) return; switch(toupper(*lin1)) -@@ -669,7 +670,7 @@ +@@ -677,7 +678,7 @@ fprintf(stdout,"\n"); fprintf(stdout," H. HELP\n\n\n"); @@ -73,7 +73,7 @@ if(*lin2 == EOS) return; switch(toupper(*lin2)) { -@@ -752,7 +753,7 @@ +@@ -766,7 +767,7 @@ fprintf(stdout,"\n"); fprintf(stdout," H. HELP\n\n\n"); @@ -82,7 +82,7 @@ if(*lin2 == EOS) return; switch(toupper(*lin2)) { -@@ -886,7 +887,7 @@ +@@ -907,7 +908,7 @@ fprintf(stdout," H. HELP\n\n\n"); @@ -91,7 +91,7 @@ if( *lin2 == EOS) { if(dnaflag) { dna_pw_go_penalty = pw_go_penalty; -@@ -1008,7 +1009,7 @@ +@@ -1029,7 +1030,7 @@ fprintf(stdout," 8. Protein Gap Parameters\n\n"); fprintf(stdout," H. HELP\n\n\n"); @@ -100,7 +100,7 @@ if(*lin2 == EOS) { if(dnaflag) { -@@ -1101,7 +1102,7 @@ +@@ -1122,7 +1123,7 @@ fprintf(stdout," 5. Toggle End Gap Separation :%s\n\n",(!use_endgaps) ? "OFF" : "ON"); fprintf(stdout," H. HELP\n\n\n"); @@ -109,7 +109,7 @@ if(*lin2 == EOS) return; -@@ -1115,7 +1116,7 @@ +@@ -1136,7 +1137,7 @@ case '3': fprintf(stdout,"Hydrophilic Residues Currently: %s\n",hyd_residues); @@ -118,7 +118,7 @@ if (*lin1 != EOS) { for (i=0;i= PAGE_LEN) { - fprintf(stdout,"\n"); -- getstr("Press [RETURN] to continue or X to stop",lin2); -+ getstr("Press [RETURN] to continue or X to stop",lin2,MAXLINE); - if(toupper(*lin2) == 'X') { - fclose(help_file); - return; -@@ -1194,7 +1194,7 @@ - } - if(usemenu) { - fprintf(stdout,"\n"); -- getstr("Press [RETURN] to continue",lin2); -+ getstr("Press [RETURN] to continue",lin2,MAXLINE); - } - fclose(help_file); - } -@@ -1232,7 +1232,7 @@ - ++nlines; - if(nlines >= PAGE_LEN) { - fprintf(stdout,"\n"); -- getstr("Press [RETURN] to continue or X to stop",lin2); -+ getstr("Press [RETURN] to continue or X to stop",lin2,MAXLINE); - if(toupper(*lin2) == 'X') { - fclose(file); - return; -@@ -1243,7 +1243,7 @@ - } - fclose(file); - fprintf(stdout,"\n"); -- getstr("Press [RETURN] to continue",lin2); -+ getstr("Press [RETURN] to continue",lin2,MAXLINE); - } - - -@@ -1692,7 +1692,7 @@ - FILE *infile; - - if(usemenu) -- getstr("Enter name of the matrix file",lin2); -+ getstr("Enter name of the matrix file",lin2,MAXLINE); - else - strcpy(lin2,str); - -@@ -1718,7 +1718,7 @@ - FILE *infile; - - if(usemenu) -- getstr("Enter name of the matrix file",lin2); -+ getstr("Enter name of the matrix file",lin2,MAXLINE); - else - strcpy(lin2,str); - -@@ -2121,7 +2121,7 @@ - strcpy(local_prompt,"\n\nEnter new name to avoid overwriting "); - strcat(local_prompt," [%s]: "); - fprintf(stdout,local_prompt,file_name); -- gets(temp); -+ fgets(temp,FILENAMELEN+1,stdin); - if(*temp != EOS) strcpy(file_name,temp); - } - } -@@ -2129,7 +2129,7 @@ - strcpy(local_prompt,prompt); - strcat(local_prompt," [%s]: "); - fprintf(stdout,local_prompt,file_name); -- gets(temp); -+ fgets(temp,FILENAMELEN+1,stdin); - if(*temp != EOS) strcpy(file_name,temp); - } - -@@ -2335,7 +2335,7 @@ - if (usemenu) - fprintf(stdout,"\nUse the existing GUIDE TREE file, %s (y/n) ? [y]: ", - tree_name); -- gets(temp); -+ fgets(temp,MAXLINE,stdin); - if(*temp != 'n' && *temp != 'N') { - strcpy(phylip_name,tree_name); - use_tree = TRUE; -@@ -2567,7 +2567,7 @@ - - fprintf(stdout,"\nEnter a name for the guide tree file [%s]: ", - phylip_name); -- gets(temp); -+ fgets(temp,MAXLINE,stdin); - if(*temp != EOS) - strcpy(phylip_name,temp); - } -@@ -2676,7 +2676,7 @@ - #endif - fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 1, %s (y/n) ? [y]: ", - tree_name); -- gets(temp); -+ fgets(temp,MAXLINE,stdin); - if(*temp != 'n' && *temp != 'N') { - strcpy(p1_tree_name,tree_name); - use_tree1 = TRUE; -@@ -2702,7 +2702,7 @@ - #endif - fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 2, %s (y/n) ? [y]: ", - tree_name); -- gets(temp); -+ fgets(temp,MAXLINE,stdin); - if(*temp != 'n' && *temp != 'N') { - strcpy(p2_tree_name,tree_name); - use_tree2 = TRUE; -@@ -3730,7 +3730,7 @@ - if(usemenu) { - fprintf(stdout,"\nEnter a name for the parameter output file [%s]: ", - parname); -- gets(temp); -+ fgets(temp,FILENAMELEN+1,stdin); - if(*temp != EOS) - strcpy(parname,temp); - } diff --git a/biology/clustalw/files/patch-ah b/biology/clustalw/files/patch-ah index e16d4f3b28d9..929da1599634 100644 --- a/biology/clustalw/files/patch-ah +++ b/biology/clustalw/files/patch-ah @@ -1,6 +1,6 @@ ---- sequence.c-orig Thu Mar 21 10:22:35 2002 -+++ sequence.c Thu Mar 21 10:22:53 2002 -@@ -922,7 +922,7 @@ +--- sequence.c.orig Thu Feb 13 15:27:06 2003 ++++ sequence.c Thu Feb 13 15:27:37 2003 +@@ -924,7 +924,7 @@ static Boolean dnaflag1; if(usemenu) diff --git a/biology/clustalw/files/patch-ai b/biology/clustalw/files/patch-ai index a228ed5b1eb4..d2f63dc9e0e5 100644 --- a/biology/clustalw/files/patch-ai +++ b/biology/clustalw/files/patch-ai @@ -1,6 +1,6 @@ ---- trees.c-orig Thu Mar 21 10:23:04 2002 -+++ trees.c Thu Mar 21 10:23:20 2002 -@@ -845,7 +845,7 @@ +--- trees.c.orig Thu Feb 13 15:52:06 2003 ++++ trees.c Thu Feb 13 16:19:08 2003 +@@ -1497,7 +1497,7 @@ fprintf(stdout,"\n or 3) use the PHYLIP package."); fprintf(stdout,"\n\n"); if (usemenu) diff --git a/biology/clustalw/files/patch-aj b/biology/clustalw/files/patch-aj index d5881bdb2c03..4e7cb3c21c94 100644 --- a/biology/clustalw/files/patch-aj +++ b/biology/clustalw/files/patch-aj @@ -1,6 +1,6 @@ ---- util.c-orig Thu Mar 21 10:15:59 2002 -+++ util.c Thu Mar 21 10:17:11 2002 -@@ -171,10 +171,10 @@ +--- util.c.orig Thu Feb 13 16:19:35 2003 ++++ util.c Thu Feb 13 16:21:40 2003 +@@ -171,10 +171,11 @@ return str; } @@ -10,10 +10,11 @@ fprintf(stdout,"%s: ",instr); - gets(outstr); + fgets(outstr, len, stdin); ++ outstr[strlen(outstr)-1] = '\0'; } double getreal(char *instr,double minx,double maxx,double def) -@@ -185,7 +185,7 @@ +@@ -185,7 +186,7 @@ while(TRUE) { fprintf(stdout,"%s (%.1f-%.1f) [%.1f]: ",instr,minx,maxx,def); @@ -22,7 +23,7 @@ status=sscanf(line,"%f",&ret); if(status == EOF) return def; if(ret>maxx) { -@@ -210,7 +210,7 @@ +@@ -210,7 +211,7 @@ while(TRUE) { fprintf(stdout,"%s (%d..%d) [%d]: ", instr,(pint)minx,(pint)maxx,(pint)def); @@ -31,7 +32,7 @@ status=sscanf(line,"%d",&ret); if(status == EOF) return def; if(ret>maxx) { -@@ -230,7 +230,7 @@ +@@ -230,7 +231,7 @@ { char line[MAXLINE]; diff --git a/biology/clustalw/files/patch-ak b/biology/clustalw/files/patch-ak deleted file mode 100644 index 8bad3e0dfbbb..000000000000 --- a/biology/clustalw/files/patch-ak +++ /dev/null @@ -1,10 +0,0 @@ ---- util.c-orig Fri Mar 22 09:30:46 2002 -+++ util.c Fri Mar 22 09:31:33 2002 -@@ -175,6 +175,7 @@ - { - fprintf(stdout,"%s: ",instr); - fgets(outstr, len, stdin); -+ outstr[strlen(outstr)-1] = '\0'; - } - - double getreal(char *instr,double minx,double maxx,double def) diff --git a/biology/clustalw/pkg-comment b/biology/clustalw/pkg-comment deleted file mode 100644 index 96dce0a32542..000000000000 --- a/biology/clustalw/pkg-comment +++ /dev/null @@ -1 +0,0 @@ -CLUSTAL W Multiple Sequence Alignment Program