--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* gki.c
+ * SRE, Sat May 1 14:49:08 1999
+ *
+ * "generic key index" module: emulation of Perl hashes.
+ * Maps keys (ASCII char strings) to array index. Dynamically
+ * resizes the hash table.
+ *
+ * Limitations:
+ * - hash table can only grow; no provision for deleting keys
+ * or downsizing the hash table.
+ * - Maximum hash table size set at 100003. Performance
+ * will degrade for key sets much larger than this.
+ * - Assumes that integers are 32 bits (or greater).
+ *
+ * Defines a typedef'd structure:
+ * gki - a key index hash table.
+ * Provides functions:
+ * GKIInit() - start a hash table.
+ * GKIStoreKey() - store a new key, get a unique index.
+ * GKIKeyIndex() - retrieve an existing key's index.
+ * GKIFree() - free a hash table.
+ * GKIStatus() - Debugging: prints internal status of a hash struct
+ *
+ *
+ * Note that there are no dependencies on squid; the gki.c/gki.h
+ * pair are base ANSI C and can be reused anywhere.
+ *****************************************************************
+ *
+ * API for storing/reading stuff:
+ * moral equivalent of Perl's $foo{$key} = whatever, $bar{$key} = whatever:
+ * #include "gki.h"
+ *
+ * gki *hash;
+ * int idx;
+ * char *key;
+ *
+ * hash = GKIInit();
+ * (Storing:)
+ * (foreach key) {
+ * idx = GKIStoreKey(hash, key);
+ * (reallocate foo, bar as needed)
+ * foo[idx] = whatever;
+ * bar[idx] = whatever;
+ * }
+ * (Reading:)
+ * (foreach key) {
+ * idx = GKIKeyIndex(hash, key);
+ * if (idx == -1) {no_such_key; }
+ * (do something with) foo[idx];
+ * (do something with) bar[idx];
+ * }
+ * GKIFree();
+ *
+ *****************************************************************
+ *
+ * Timings on wrasse for 45402 keys in /usr/dict/words using
+ * Tests/test_gki:
+ * 250 msec store (6 usec/store)
+ * 140 msec retrieve (3 usec/retrieve)
+ * and using the 13408 names of Pfam's GP120.full alignment:
+ * 70 msec store (5 usec/store)
+ * 50 msec retrieve (4 usec/retrieve)
+ *
+ * RCS $Id: gki.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: gki.c,v 1.3 2000/12/21 23:42:59 eddy Exp)
+ */
+
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
+#include "squid.h"
+#include "gki.h"
+
+/*
+ * Best hash table sizes are prime numbers (see Knuth vol 3, Sorting
+ * and Searching).
+ * gki_primes[] defines the ascending order of hash table sizes
+ * that we use in upsizing the hash table dynamically.
+ * useful site for testing primes:
+ * http://www.idbsu.edu/people/jbrennan/algebra/numbers/sieve.html
+ * Because of the way gki_hashvalue works, the largest number
+ * must be < INT_MAX / 128 / 128 : 131072 on a 32 bit machine.
+ */
+static int gki_primes[] = { 101, 1009, 10007, 100003 };
+#define GKI_NPRIMES 4
+#define GKI_ALPHABETSIZE 128
+
+static GKI *gki_alloc(int primelevel);
+static int gki_hashvalue(GKI *hash, char *key);
+static int gki_upsize(GKI *old);
+
+
+/* Function: GKIInit()
+ * Date: SRE, Sat May 1 11:12:24 1999 [May Day geek-out]
+ *
+ * Purpose: Initialize a hash table for key indexing.
+ * Simply a wrapper around a level 0 gki_alloc().
+ *
+ * Args: (void)
+ *
+ * Returns: An allocated hash table structure.
+ * Caller frees with GKIFree().
+ */
+GKI *
+GKIInit(void)
+{
+ GKI *hash;
+ hash = gki_alloc(0);
+ return hash;
+}
+
+/* Function: GKIFree()
+ * Date: SRE, Sat May 1 11:13:26 1999 [May Day geek-out]
+ *
+ * Purpose: Free a key index hash table.
+ *
+ * Args: hash - the gki structure
+ *
+ * Returns: (void).
+ * hash table is destroyed.
+ */
+void
+GKIFree(GKI *hash)
+{
+ struct gki_elem *ptr;
+ int i;
+
+ if (hash == NULL) return; /* tolerate a NULL */
+
+ for (i = 0; i < hash->nhash; i++)
+ while (hash->table[i] != NULL)
+ {
+ ptr = hash->table[i]->nxt;
+ /* NULL keys can occur after we've gki_upsize'd */
+ if (hash->table[i]->key != NULL) free(hash->table[i]->key);
+ free(hash->table[i]);
+ hash->table[i] = ptr;
+ }
+ free(hash->table);
+ free(hash);
+}
+
+/* Function: GKIStoreKey()
+ * Date: SRE, Sat May 1 11:16:48 1999 [May Day geek-out]
+ *
+ * Purpose: Store a key in the key index hash table.
+ * Associate it with a unique "key index", counting
+ * from 0. (It's this index that lets us map
+ * the hashed keys to indexed C arrays, (clumsily)
+ * emulating Perl's hashes.)
+ *
+ * Does *not* check to see if the key's already
+ * in the table, so it's possible to store multiple
+ * copies of a key with different indices; probably
+ * not what you want, so if you're not sure the
+ * key is unique, check the table first with
+ * GKIKeyIndex().
+ *
+ * Args: hash - GKI structure to store the key in
+ * key - string to store
+ *
+ * Returns: the new key's index. Since it's always the
+ * last one in the current array, this index is
+ * just hash->nkeys-1.
+ * On a malloc failure, returns -1.
+ * hash table is modified.
+ */
+int
+GKIStoreKey(GKI *hash, char *key)
+{
+ int val;
+ struct gki_elem *ptr;
+
+ val = gki_hashvalue(hash, key);
+
+ ptr = hash->table[val];
+ hash->table[val] = MallocOrDie(sizeof(struct gki_elem));
+ hash->table[val]->key = MallocOrDie(sizeof(char) * (strlen(key)+1));
+ strcpy(hash->table[val]->key, key);
+
+ hash->table[val]->idx = hash->nkeys;
+ hash->table[val]->nxt = ptr;
+
+ hash->nkeys++;
+ /* time to upsize? */
+ if (hash->nkeys > 3*hash->nhash && hash->primelevel < GKI_NPRIMES-1)
+ gki_upsize(hash);
+
+ return hash->nkeys-1;
+}
+
+/* Function: GKIKeyIndex()
+ * Date: SRE, Sat May 1 11:20:42 1999 [May Day geek-out]
+ *
+ * Purpose: Look up a key in the hash table. Return
+ * its index (0..nkeys-1), else -1 if the key
+ * isn't in the hash (yet).
+ *
+ * Args: hash - the GKI hash table to search in
+ * key - the key to look up
+ *
+ * Returns: -1 if key is not found;
+ * index of key if it is found (range 0..nkeys-1).
+ * hash table is unchanged.
+ */
+int
+GKIKeyIndex(GKI *hash, char *key)
+{
+ struct gki_elem *ptr;
+ int val;
+
+ val = gki_hashvalue(hash, key);
+ for (ptr = hash->table[val]; ptr != NULL; ptr = ptr->nxt)
+ if (strcmp(key, ptr->key) == 0) return ptr->idx;
+ return -1;
+}
+
+/* Function: GKIStatus()
+ * Date: SRE, Sat May 1 11:11:13 1999 [St. Louis]
+ *
+ * Purpose: (DEBUGGING) How are we doing? Calculate some
+ * simple statistics for the hash table.
+ *
+ * Args: hash - the GKI hash table to look at
+ *
+ * Returns: (void)
+ * Prints diagnostics on stdout.
+ * hash table is unchanged.
+ */
+void
+GKIStatus(GKI *hash)
+{
+ struct gki_elem *ptr;
+ int i;
+ int nkeys;
+ int nempty = 0;
+ int maxkeys = -1;
+ int minkeys = INT_MAX;
+
+ for (i = 0; i < hash->nhash; i++)
+ {
+ nkeys = 0;
+ for (ptr = hash->table[i]; ptr != NULL; ptr = ptr->nxt)
+ nkeys++;
+
+ if (nkeys == 0) nempty++;
+ if (nkeys > maxkeys) maxkeys = nkeys;
+ if (nkeys < minkeys) minkeys = nkeys;
+ }
+
+ printf("Total keys: %d\n", hash->nkeys);
+ printf("Hash table size: %d\n", hash->nhash);
+ printf("Average occupancy: %.1f\n", (float) hash->nkeys / (float) hash->nhash);
+ printf("Unoccupied slots: %d\n", nempty);
+ printf("Most in one slot: %d\n", maxkeys);
+ printf("Least in one slot: %d\n", minkeys);
+
+}
+
+
+/* Function: gki_alloc()
+ * Date: SRE, Sat May 1 11:55:47 1999 [May Day geek-out]
+ *
+ * Purpose: Allocate a hash table structure with the
+ * size given by primelevel.
+ *
+ * Args: primelevel - level 0..GKI_NPRIMES-1, specifying
+ * the size of the table; see gki_primes[]
+ * array.
+ *
+ * Returns: An allocated hash table structure.
+ * Caller frees with GKIFree().
+ */
+static GKI *
+gki_alloc(int primelevel)
+{
+ GKI *hash;
+ int i;
+
+ if (primelevel < 0 || primelevel >= GKI_NPRIMES)
+ Die("bad primelevel in gki_alloc()");
+ hash = MallocOrDie(sizeof(GKI));
+
+ hash->primelevel = primelevel;
+ hash->nhash = gki_primes[hash->primelevel];
+ hash->table = MallocOrDie(sizeof(struct gki_elem) * hash->nhash);
+ for (i = 0; i < hash->nhash; i++)
+ hash->table[i] = NULL;
+ hash->nkeys = 0;
+ return hash;
+}
+
+
+/* Function: gki_hashvalue()
+ * Date: SRE, Sat May 1 11:14:10 1999 [May Day geek-out]
+ *
+ * Purpose: Calculate the hash value for a key. Usually
+ * we expect a one-word key, but the function will
+ * hash any ASCII string effectively. The hash function
+ * is a simple one (see p. 233 of Sedgewick,
+ * Algorithms in C).
+ * Slightly optimized: does two characters at a time
+ * before doing the modulo; this gives us a significant
+ * speedup.
+ *
+ * Args: hash - the gki structure (we need to know the hash table size)
+ * key - a string to calculate the hash value for
+ *
+ * Returns: a hash value, in the range 0..hash->nhash-1.
+ * hash table is unmodified.
+ */
+static int
+gki_hashvalue(GKI *hash, char *key)
+{
+ int val = 0;
+
+ for (; *key != '\0'; key++)
+ {
+ val = GKI_ALPHABETSIZE*val + *key;
+ if (*(++key) == '\0') { val = val % hash->nhash; break; }
+ val = (GKI_ALPHABETSIZE*val + *key) % hash->nhash;
+ }
+ return val;
+}
+
+/* Function: gki_upsize()
+ * Date: SRE, Sat May 1 11:46:07 1999 [May Day geek-out]
+ *
+ * Purpose: Grow the hash table to the next available size.
+ *
+ * Args: old - the GKI hash table to reallocate.
+ *
+ * Returns: 1 on success (the hash table is changed);
+ * 0 on failure; the table is already at its maximum size,
+ * and the hash table is returned unchanged.
+ */
+static int
+gki_upsize(GKI *old)
+{
+ GKI *new;
+ int i;
+ struct gki_elem *optr;
+ struct gki_elem *nptr;
+ int val;
+
+ if (old->primelevel >= GKI_NPRIMES-1) return 0;
+ new = gki_alloc(old->primelevel+1);
+
+ /* Read the old, store in the new, while *not changing*
+ * any key indices. Because of the way the lists are
+ * treated as LIFO stacks, all the lists are reversed
+ * in the new structure.
+ */
+ for (i = 0; i < old->nhash; i++)
+ {
+ optr = old->table[i];
+ while (optr != NULL)
+ {
+ val = gki_hashvalue(new, optr->key);
+
+ nptr = new->table[val];
+ new->table[val] = optr;
+ optr = optr->nxt;
+ new->table[val]->nxt = nptr;
+ }
+ }
+ free(old->table);
+
+ /* Now swap within the interior of the structures, so the old
+ * structure is updated to the new structure.
+ * (nkeys is identical, so we don't need to swap that element.)
+ */
+ old->primelevel = new->primelevel;
+ old->nhash = new->nhash;
+ old->table = new->table;
+ free(new);
+ return 1;
+}
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