Boolean LIBCALL StrToInt4 (CharPtr str, Int4Ptr longval)
{
Nlm_Char ch;
Nlm_Int2 i;
Nlm_Int2 len;
Nlm_Char local [64];
Nlm_Boolean nodigits;
Nlm_Boolean rsult;
long int val;
rsult = FALSE;
if (longval != NULL) {
*longval = (Nlm_Int4) 0;
}
len = (Nlm_Int2) Nlm_StringLen (str);
if (len != 0) {
rsult = TRUE;
nodigits = TRUE;
for (i = 0; i < len; i++) {
ch = str [i];
if (ch == ' ' || ch == '+' || ch == '-') {
} else if (ch < '0' || ch > '9') {
rsult = FALSE;
} else {
nodigits = FALSE;
}
}
if (nodigits) {
rsult = FALSE;
}
if (rsult && longval != NULL) {
Nlm_StringNCpy (local, str, sizeof (local));
if (sscanf (local, "%ld", &val) == 1) {
*longval = val;
}
}
}
return rsult;
}
/** GET_MATRIX_PATH callback to find the path to a specified matrix.
* Looks first in current directory, then one specified by
* .ncbirc, then in local data directory, then env
* variables.
* @param matrix_name name of the matrix (e.g., BLOSUM50) [in]
* @param is_prot protein matrix if TRUE [in]
* @return path to matrix if found, or NULL.
*/
static char*
s_BlastFindMatrixPath(const char* matrix_name, Boolean is_prot)
{
char* matrix_path = NULL; /* return value. */
char buf_path[PATH_MAX]; /* Used for path without matrix filename. */
char buf_full[PATH_MAX]; /* used for full path with filename. */
char* ptr = NULL;
if (matrix_name == NULL)
return NULL;
/* current directory */
if (Nlm_FileLength((char*) matrix_name) > 0)
{
char buf_path_2[PATH_MAX];
Nlm_ProgramPath(buf_path, PATH_MAX);
ptr = StringRChr (buf_path, DIRDELIMCHR);
if (ptr != NULL)
*ptr = '\0';
sprintf(buf_path_2, "%s%s", buf_path, DIRDELIMSTR);
matrix_path = StringSave(buf_path_2);
return matrix_path;
}
/* local data directory. */
sprintf(buf_full, "data%s%s", DIRDELIMSTR, matrix_name);
if (Nlm_FileLength(buf_full) > 0)
{
char buf_path_2[PATH_MAX];
Nlm_ProgramPath(buf_path, PATH_MAX);
ptr = StringRChr (buf_path, DIRDELIMCHR);
if (ptr != NULL)
*ptr = '\0';
sprintf(buf_path_2, "%s%sdata%s", buf_path, DIRDELIMSTR, DIRDELIMSTR);
matrix_path = StringSave(buf_path_2);
return matrix_path;
}
if(FindPath("ncbi", "ncbi", "data", buf_path, PATH_MAX)) {
sprintf(buf_full, "%s%s", buf_path, matrix_name);
if(FileLength(buf_full) > 0) {
matrix_path = StringSave(buf_path);
return matrix_path;
} else {
char alphabet_type[3]; /* aa or nt */
if (is_prot)
Nlm_StringNCpy(alphabet_type, "aa", 2);
else
Nlm_StringNCpy(alphabet_type, "nt", 2);
alphabet_type[2] = NULLB;
sprintf(buf_full, "%s%s%s%s", buf_path,
alphabet_type, DIRDELIMSTR, matrix_name);
if(FileLength(buf_full) > 0)
{
matrix_path = StringSave(buf_path);
return matrix_path;
}
}
}
return NULL;
}
static Boolean
LoadMMDBIdx(CharPtr db, CharPtr idx)
{
FILE *f;
Char fullpath [PATH_MAX];
CharPtr ptr;
Char pcBuf[100];
CharPtr pcTest;
Char pcMmdb[20];
Char pcPdb[20];
Uint4Ptr pU4Pdb;
Int4Ptr pI4Mmdb;
long count = 0;
long mmdbid = 0;
/* StrToLong stuff */
Nlm_Char ch;
Nlm_Int2 i;
Nlm_Int2 len;
Nlm_Char local [64];
Nlm_Boolean nodigits;
Nlm_Boolean rsult;
long int val;
StringCpy(fullpath, db);
StringCat(fullpath, idx);
if ((f = FileOpen (fullpath, "r")) == NULL)
{
ErrPostEx(SEV_FATAL,0,0, "MMDBInit - Failed to load MMDB index - check config file.");
return FALSE;
}
pcTest = fgets(pcBuf, (size_t)100, f);
if (pcTest)
{
sscanf(pcBuf, "%ld", &iMMDBSize);
}
if ((iMMDBSize == 0) || (iMMDBSize > 100000))
{
ErrPostEx(SEV_FATAL,0,0, "Internal - LoadMMDBIdx() Failure 2;");
return FALSE;
}
pI4Mmdbidx = (Int4Ptr) MemNew((size_t) ((iMMDBSize)*sizeof(Int4)));
pU4Pdbidx = (Uint4Ptr) MemNew((size_t) ((iMMDBSize)*sizeof(Uint4)));
if ((!pI4Mmdbidx) || (!pU4Pdbidx))
{
ErrPostEx(SEV_FATAL,0,0, "Internal - LoadMMDBIdx() Out of Memory;");
return FALSE;
}
pI4Mmdb = pI4Mmdbidx;
pU4Pdb = pU4Pdbidx;
do
{
pcBuf[0] = '\0';
pcTest = fgets(pcBuf, (size_t)100, f);
if (pcTest)
{
sscanf(pcBuf, "%s%s", pcMmdb , pcPdb);
StrUpper(pcPdb);
mmdbid = 0;
/* this is code from Nlm StrToLong */
rsult = FALSE;
len = (Nlm_Int2) Nlm_StringLen (pcMmdb);
if (len != 0) {
rsult = TRUE;
nodigits = TRUE;
for (i = 0; i < len; i++) {
ch = pcMmdb [i];
if (ch == ' ' || ch == '+' || ch == '-') {
} else if (ch < '0' || ch > '9') {
rsult = FALSE;
} else {
nodigits = FALSE;
}
}
if (nodigits) {
rsult = FALSE;
}
if (rsult) {
Nlm_StringNCpy (local, pcMmdb, sizeof (local));
if (sscanf (local, "%ld", &val) == 1) {
mmdbid = val;
}
}
}
/* printf("%ld %s %ld %ld\n", mmdbid, pcPdb, (long) count, (long) iMMDBSize-1); */
if ((mmdbid == 0) || (StringLen(pcPdb) > 4))
{
MMDBFini();
ErrPostEx(SEV_FATAL,0,0, "Internal - LoadMMDBIdx() Bad Index Values");
return FALSE;
}
*pI4Mmdb = mmdbid;
*pU4Pdb = HashPDBCode(pcPdb);
pI4Mmdb++;
pU4Pdb++;
count++;
}
if (count > (iMMDBSize))
{
MMDBFini();
ErrPostEx(SEV_FATAL,0,0, "Internal - LoadMMDBIdx() Index count is wrong at top of file;");
return FALSE;
}
} while (pcTest);
FileClose(f);
return TRUE;
}