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Code Issues Releases Activity

Update to 1.83.

Browse Source 
PR:		48264
Submitted by:	David A. Bader <dbader@eece.unm.edu>
This commit is contained in:
Christian Weisgerber 2003-02-15 18:43:14 +00:00
parent 3a4333e34d
commit 97d4b58c28
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=75592
13 changed files with 179 additions and 182 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
biology/clustalw/Makefile
View File

@ -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}

2
biology/clustalw/distinfo
View File

@ -1 +1 @@
MD5 (clustalw1.82.UNIX.tar.gz) = 8171ec890182383000bdb83de3022ca2
MD5 (clustalw1.83.UNIX.tar.gz) = dc240277e5bb14ffc106d4a5fda87752

6
biology/clustalw/files/patch-aa
View File

@ -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

15
biology/clustalw/files/patch-ab
View File

@ -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

132
biology/clustalw/files/patch-ac
View File

@ -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);
}

32
biology/clustalw/files/patch-ae
View File

@ -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<strlen(hyd_residues) && i<26;i++) {
c = lin1[i];
@@ -1167,7 +1168,7 @@
@@ -1188,7 +1189,7 @@
fprintf(stdout,"--\n");
@ -127,7 +127,7 @@
if(*lin2 == EOS) return(matn);
i=toupper(*lin2)-'0';
@@ -1202,7 +1203,7 @@
@@ -1223,7 +1224,7 @@
fprintf(stdout,"\n%s\n",title);
strcpy(line,prompt);
strcat(line, "(y/n) ? [y]");

6
biology/clustalw/files/patch-af
View File

@ -1,6 +1,6 @@
--- clustalw.h-orig Thu Mar 21 10:15:28 2002
+++ clustalw.h Thu Mar 21 10:15:43 2002
@@ -234,7 +234,7 @@
--- clustalw.h.orig Thu Feb 13 15:21:45 2003
+++ clustalw.h Thu Feb 13 15:21:57 2003
@@ -238,7 +238,7 @@
char *blank_to_(char *str);
char *upstr(char *str);
char *lowstr(char *str);

128
biology/clustalw/files/patch-ag
View File

@ -1,128 +0,0 @@
--- interface.c-orig Thu Mar 21 10:19:26 2002
+++ interface.c Thu Mar 21 10:22:18 2002
@@ -1170,7 +1170,7 @@
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;
@@ -1182,7 +1182,7 @@
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;
@@ -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);
}

6
biology/clustalw/files/patch-ah
View File

@ -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)

6
biology/clustalw/files/patch-ai
View File

@ -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)

13
biology/clustalw/files/patch-aj
View File

@ -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];

10
biology/clustalw/files/patch-ak
View File

@ -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)

1
biology/clustalw/pkg-comment
View File

@ -1 +0,0 @@
CLUSTAL W Multiple Sequence Alignment Program