biology/cdbfasta: Update to 2018.10.05

Fix build for c++17
Improve pkg-descr
Add license

Reported by:    pkg-fallout

1 files changed, 98 insertions, 0 deletions

diff --git a/biology/cdbfasta/files/patch-gclib_GStr.cpp b/biology/cdbfasta/files/patch-gclib_GStr.cpp
new file mode 100644
index 000000000000..1aa3a5f8f739
--- /dev/null
+++ b/biology/cdbfasta/files/patch-gclib_GStr.cpp
@@ -0,0 +1,98 @@
+--- gclib/GStr.cpp.orig	2023-07-10 09:57:46 UTC
++++ gclib/GStr.cpp
+@@ -424,8 +424,8 @@ GStr& GStr::trim(char c) {
+   }
+ 
+ GStr& GStr::trim(char c) {
+- register int istart;
+- register int iend;
++ int istart;
++ int iend;
+  for (istart=0; istart<length() && my_data->chars[istart]==c;istart++) ;
+  if (istart==length()) {
+        make_unique(); //edit operation ahead
+@@ -444,8 +444,8 @@ GStr& GStr::trim(const char* c) {
+  }
+ 
+ GStr& GStr::trim(const char* c) {
+- register int istart;
+- register int iend;
++ int istart;
++ int iend;
+  for (istart=0; istart<length() && strchr(c, my_data->chars[istart])!=NULL ;istart++) ;
+  if (istart==length()) {
+         prep_data(0); //string was entirely trimmed
+@@ -464,8 +464,8 @@ GStr& GStr::trimR(char c) {
+ 
+ GStr& GStr::trimR(char c) {
+  //only trim the right end
+- //register int istart;
+- register int iend;
++ //int istart;
++ int iend;
+  for (iend=length()-1; iend>=0 && my_data->chars[iend]==c;iend--) ;
+  if (iend==-1) {
+        make_unique();
+@@ -488,7 +488,7 @@ GStr& GStr::trimR(const char* c) {
+  }
+ 
+ GStr& GStr::trimR(const char* c) {
+- register int iend;
++ int iend;
+  for (iend=length()-1; iend>=0 && strchr(c,my_data->chars[iend])!=NULL;iend--) ;
+  if (iend==-1) {
+        make_unique();
+@@ -511,7 +511,7 @@ GStr& GStr::chomp(const char* cstr) {
+ 
+ 
+ GStr& GStr::chomp(const char* cstr) {
+- register int iend;
++ int iend;
+  if (cstr==NULL || *cstr==0) return *this;
+  //check if this ends with cstr
+  int cend=strlen(cstr)-1;
+@@ -537,7 +537,7 @@ GStr& GStr::trimL(char c) {
+  }
+ 
+ GStr& GStr::trimL(char c) {
+- register int istart;
++ int istart;
+  for (istart=0; istart<length() && my_data->chars[istart]==c;istart++) ;
+  if (istart==length()) {
+        prep_data(0); //string was entirely trimmed
+@@ -554,7 +554,7 @@ GStr& GStr::trimL(const char* c) {
+  }
+ 
+ GStr& GStr::trimL(const char* c) {
+- register int istart;
++ int istart;
+  for (istart=0; istart<length() && strchr(c,my_data->chars[istart])!=NULL;istart++) ;
+  if (istart==length()) {
+        prep_data(0); //string was entirely trimmed
+@@ -700,7 +700,7 @@ bool GStr::is_space() const {
+     if (my_data == &null_data)
+         return false;
+ 
+-    for (register const char *p = my_data->chars; *p; p++)
++    for (const char *p = my_data->chars; *p; p++)
+         if (!isspace(*p))
+             return false;
+ 
+@@ -1083,7 +1083,7 @@ GStr& GStr::upper() {
+ 
+ GStr& GStr::upper() {
+   make_unique(); //edit operation ahead
+-  for (register char *p = chrs(); *p; p++)
++  for (char *p = chrs(); *p; p++)
+             *p = (char) toupper(*p);
+ 
+     return *this;
+@@ -1094,7 +1094,7 @@ GStr& GStr::lower() {
+ GStr& GStr::lower() {
+     make_unique();
+ 
+-    for (register char *p = chrs(); *p; p++)
++    for (char *p = chrs(); *p; p++)
+           *p = (char) tolower(*p);
+ 
+     return *this;