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/*****************************************************************
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* SQUID - a library of functions for biological sequence analysis
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* Copyright (C) 1992-2002 Washington University School of Medicine
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* This source code is freely distributed under the terms of the
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* GNU General Public License. See the files COPYRIGHT and LICENSE
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*****************************************************************/
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* SRE, Wed Jun 19 11:19:22 1996
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* File operation utilities, dealing with pathnames, directories,
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* and environment variables.
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* The goal is to have these be platform-independent but they
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* currently are UNIX-specific: i.e. this file is currently POSIX compliant
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* but it is NOT ANSI C compliant. (The sole offender is getenv().)
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* RCS $Id: file.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: file.c,v 1.8 2002/03/07 03:18:02 eddy Exp)
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* VMS: #define DIRSLASH ']'
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* MacOS: #define DIRSLASH ':'
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* DOS: #define DIRSLASH '\\'
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* The code assumes that '.' is used for file name extensions,
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#define DIRSLASH '/' /* UNIX directory paths have /foo/bar */
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/* Function: FileDirname()
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* Purpose: Returns the path from a filename:
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* "/foo/bar/baz" -> "/foo/bar"
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* i.e. the string will be non-NULL; it will
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* contain the string up to but not including the
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* last '/' character; returns "." if
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* there are no '/' characters, and returns "/"
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* if the last slash is the first character.
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* Modeled on Tcl's "file dirname" command.
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* Args: file - name of file "/foo/bar/baz".
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* Return: ptr to malloc'ed string "/foo/bar".
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FileDirname(char *file)
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lastslash = strrchr(file, DIRSLASH);
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len = (lastslash == NULL) ? 0 : (int) (lastslash - file);
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dirname = (char *) MallocOrDie (sizeof(char) * (len+2));
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if (len > 0) strncpy(dirname, file, len);
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else if (*file != DIRSLASH) { *dirname = '.'; len = 1; }
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else { *dirname = DIRSLASH; len = 1; }
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/* Function: FileTail()
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* Purpose: Return everything after the DIRSLASH:
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* "/foo/bar/baz.1" -> "baz.1"
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* If noextension is TRUE, removes a trailing ".foo" extension
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* Args: file - name of file "/foo/bar/baz.1"
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* noextension - TRUE to also remove extensions
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* Return: ptr to malloc'ed string "baz.1"
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FileTail(char *file, int noextension)
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/* remove directory prefix */
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lastslash = strrchr(file, DIRSLASH);
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tail = (char *) MallocOrDie (sizeof(char) * (strlen(file)+1));
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if (lastslash == NULL) strcpy(tail, file);
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else strcpy(tail, lastslash+1);
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/* remove trailing suffix */
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if ((lastdot = strrchr(tail, '.')) != NULL)
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/* Function: FileSameDirectory()
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* Date: SRE, Wed Mar 6 20:03:23 2002 [St. Louis]
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* Purpose: Given a path to one file, and the
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* name of another file in the same directory,
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* concat the path from file1 onto file2, and
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* return the result. Caller must free the ptr
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* Written for SSI - SSI indices contain filenames
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* without paths, and we will need to convert that
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* Args: file1 - a path to a file, e.g. "/foo/bar/baz.1"
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* file2 - a simple filename, e.g. "quux.2"
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* Returns: path to file2: e.g. "/foo/bar/quux.2"
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* Returns NULL if file2 already has a path, and the result
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* would be a different place.
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FileSameDirectory(char *file1, char *file2)
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path = FileDirname(file1);
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tail = FileTail(file2, FALSE);
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if (strcmp(file2, tail) != 0) seems_ok = 0; /* ut-oh, file2 *had* a path */
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result = FileConcat(path, tail);
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if (! seems_ok && strcmp(result, file2) != 0) {
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free(result); result = NULL;
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/* Function: FileConcat()
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* Purpose: Concatenate a directory path and a file name,
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* returning a pointer to a malloc'ed string with the
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* full filename. This isn't just a string concat,
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* because we're careful about the dir slash.
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FileConcat(char *dir, char *file)
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full = (char *) MallocOrDie (sizeof(char) * (strlen(dir)+strlen(file)+2));
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if (*file == DIRSLASH) strcpy(full, file); /* file = "/foo", ignore directory. */
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else sprintf(full, "%s%c%s", dir, DIRSLASH, file);
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/* Function: FileAddSuffix()
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* Date: SRE, Wed Aug 1 11:19:33 2001 [Pasadena]
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* Purpose: Add a suffix to a filename, return a malloc'ed
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* string containing the new filename.sfx name.
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* FileAddSuffix("genbank", "ssi")
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* returns "genbank.ssi".
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FileAddSuffix(char *filename, char *sfx)
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new = MallocOrDie(strlen(filename) + strlen(sfx) + 2);
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sprintf(new, "%s.%s", filename, sfx);
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/* Function: EnvFileOpen()
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* Date: Sun Feb 12 10:55:29 1995
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* Purpose: Open a file, given a file name and an environment
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* variable that contains a directory path. Files
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* are opened read-only. Does not look at current directory
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* unless "." is explicitly in the path specified by env.
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* fp = EnvFileOpen("BLOSUM45", "BLASTMAT", NULL);
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* fp = EnvFileOpen("swiss", "BLASTDB", NULL);
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* Environment variables may contain a colon-delimited
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* list of more than one path; e.g.
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* setenv BLASTDB /nfs/databases/foo:/nfs/databases/bar
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* Sometimes a group of files may be found in
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* one directory; for instance, an index file with a
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* database. The caller can EnvFileOpen() the main
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* file, and ask to get the name of the
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* directory back in ret_dir, so it can construct
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* the other auxiliary file names and fopen() them. (If it called
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* EnvFileOpen(), it might get confused by
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* file name clashes and open files in different
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* Args: fname - name of file to open
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* env - name of environment variable containing path
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* ret_dir - if non-NULL, RETURN: name of dir that was used.
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* Return: FILE * to open file, or NULL on failure -- same as fopen()
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* Caller must free ret_dir if it passed a non-NULL address.
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EnvFileOpen(char *fname, char *env, char **ret_dir)
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char *s; /* ptr to indiv element in env list */
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char full[1024]; /* constructed file name */
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if (env == NULL) return NULL;
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if ((path = Strdup(getenv(env))) == NULL) return NULL;
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s = strtok(path, ":");
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if (((int) strlen(fname) + (int) strlen(s) + 2) > 1024)
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{ free(path); return NULL; }
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sprintf(full, "%s%c%s", s, DIRSLASH, fname);
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if ((fp = fopen(full, "r")) != NULL) break;
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s = strtok(NULL, ":");
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/* Return the path we used, if caller wants it
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if (ret_dir != NULL) *ret_dir = Strdup(s);
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/* Function: FileExists()
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* Purpose: Return TRUE if filename exists.
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* Testing fopen() is the only possible platform-independent test
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FileExists(char *filename)
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if ((fp = fopen(filename, "r"))) { fclose(fp); return TRUE; }