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/* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* File Name: vastsubs.c
*
* Author: Tom Madej
*
* Version Creation Date: 25 March 1998
*
* $Log: vastsubs.c,v $
* Revision 6.1 1998/03/30 19:10:12 madej
* Initial version of subset filtering routines.
*
*/
/* This code implements subset filtering for the VAST structure neighbor hit lists. */
#include <stdio.h>
#include <ncbi.h>
#include <ncbimisc.h>
/* Coefficients (bases) for hash and increment functions. */
#define HBASE0 131 /* base for hash function */
#define HBASE1 3373 /* base for increment function */
#define MAXN_SUB 128 /* max number of subsets */
#define MAX_SUBNAME 64 /* max length of a subset name */
#define DOMID_SIZE 6 /* number of chars in a domain identifier */
#define NPRIMES 10 /* assortment of hash table sizes */
/* hash table nodes */
typedef struct ht_Node {
Int4 num; /* domain id array index for header, subset number for others */
Int4 grpnum; /* group number, i.e. cluster number within the subset */
Int4 grank; /* rank within the group */
struct ht_Node *next;
} HT_NODE;
static Int4 TableSize; /* size of the hash table (a prime) */
static HT_NODE *HashTable; /* the actual hash table */
static Char *DomIdArray; /* aux array for storing domain identifiers */
static Int4 NumberOfDomains; /* number of domains read in */
static Int4 NumberOfSubsets; /* number of subsets used */
static Int4 *SubsetList; /* indices for subset names */
static Char *SubsetArray; /* array for storing subset names */
static Int4 PrimeTable[NPRIMES] = { 100003, 200003, 300007, 400009, 500009, 600011, 700001,
800011, 900001, 999983 };
/* Hash function used to identify chains/domains that belong to a given subset. */
static Int4
HashDomId(Char *domid, Int4 mod0)
{
Int4 sum;
Char *p;
for (sum = 0, p = domid; *p; p++)
sum = (HBASE0*sum + (Int4) *p) % mod0;
return sum;
} /* end HashDomId */
/* Increment function used in double hashing scheme. */
static Int4
IncrDomId(Char *domid, Int4 mod0)
{
Int4 sum;
Char *p;
for (sum = 0, p = domid; *p; p++)
sum = (HBASE1*sum + (Int4) *p) % mod0;
return sum % (mod0 - 1) + 1;
} /* end IncrDomId */
/* Insert an entry into the hash table. */
static Int4
SubsetInsert(Int4 idloc, Int4 mod0, Int4 sublen, Int4 *subset, Int4 *grps, Int4 *ranks)
{
Int4 h, i, j, cnt, incr, h0;
HT_NODE *htn;
h0 = HashDomId(&DomIdArray[idloc], mod0);
incr = IncrDomId(&DomIdArray[idloc], mod0);
/* be sure to count the number of probes */
for (i = cnt = 0; cnt < mod0; i += incr, cnt++) {
h = (h0 + i) % mod0;
if (HashTable[h].num < 0) {
/* insert the entry */
HashTable[h].num = idloc;
for (j = 0; j < sublen; j++) {
htn = (HT_NODE *) MemNew(sizeof(HT_NODE));
htn->num = subset[j];
htn->grpnum = grps[j];
htn->grank = ranks[j];
htn->next = HashTable[h].next;
HashTable[h].next = htn;
}
break;
}
}
/* since the table shouldn't overflow this return will signal a bug */
if (cnt >= mod0)
return -1;
return h;
} /* end SubsetInsert */
/* Return the smallest prime from PrimeTable[] that is larger than or equal to the input.
*
* Warning: I've selected a small assortment of large primes for table sizes. If the PDB
* should ever grow so that we have more than about 250,000 domains, then we'll need to
* add some larger table sizes!
*/
static Int4
GetPrime(Int4 n)
{
Int4 i;
for (i = 0; i < NPRIMES; i++)
if (PrimeTable[i] >= n)
return PrimeTable[i];
return 0;
} /* end GetPrime */
/* Allocates space for the subset table and domain identifier array. Reads in the subset lists.
*
* Here is the format for the file that contains the subset table.
*
* 1. The first line is an integer that gives the total number of entries (domains).
* 2. The second line is an integer that gives the total number of subsets.
* 3. The the next few lines are the subset entries. There are 'k' of these lines,
* where 'k' is the integer in 2). Each subset entry consists of a subset number,
* i.e. 1 thru k, and a subset name. The subset name begins with the first non-blank
* character and ends with a newline (so blanks may appear within the name), e.g.
* "All of PDB".
* 4. The remainder of the lines are the domain entries. There are 'n' of these lines,
* where 'n' is the integer in 1). Each domain entry consists of:
* a) an 8-character domain identifier (code);
* b) an integer giving the number of subsets it belongs to;
* c) a sequence 'm' triples of integers, where 'm' is the integer in 4b);
* d) each triple in 4c) consists of a subset number, group number, and rank within
* the group.
*/
Int4 LIBCALL
LoadSubsetTable(Char *fname)
{
Int4 i, j, n, len, strindex, ndoms, nsubs;
Int4 subset[MAXN_SUB], grps[MAXN_SUB], ranks[MAXN_SUB];
FILE *fd;
Char ch, domid[9];
if ((fd = FileOpen(fname, "r")) == NULL)
return 0;
fscanf(fd, "%d", &ndoms);
NumberOfDomains = ndoms;
/* the table size should be a prime number >= 4*ndoms */
if ((TableSize = GetPrime(4*ndoms)) == 0)
return 0;
HashTable = (HT_NODE *) MemNew(TableSize*sizeof(HT_NODE));
DomIdArray = (Char *) MemNew((DOMID_SIZE + 1)*ndoms*sizeof(char));
if ((HashTable == NULL) || (DomIdArray == NULL))
return 0;
/* zap the table just to be sure */
for (i = 0; i < TableSize; i++) {
HashTable[i].num = -1;
HashTable[i].grpnum = 0;
HashTable[i].next = NULL;
}
for (i = 0; i < (DOMID_SIZE + 1)*ndoms; i++)
DomIdArray[i] = '\0';
for (i = 0; i <= DOMID_SIZE; i++)
domid[i] = '\0';
/* read in the subset numbers and names */
fscanf(fd, "%d", &nsubs);
if (nsubs > MAXN_SUB)
return 0;
NumberOfSubsets = nsubs;
SubsetList = (Int4 *) MemNew(nsubs*sizeof(Int4));
SubsetArray = (Char *) MemNew(nsubs*MAX_SUBNAME*sizeof(Char));
if ((SubsetList == NULL) || (SubsetArray == NULL))
return 0;
for (i = 0; i < nsubs; i++)
SubsetList[i] = -1;
for (i = 0, strindex = 0; i < nsubs; i++) {
if (strindex > nsubs*MAX_SUBNAME)
return 0;
fscanf(fd, "%d", &j);
if (j != i + 1)
return 0;
while (1) {
ch = (Char) fgetc(fd);
if ((ch == ' ') && (SubsetList[i] < 0))
continue;
if (SubsetList[i] < 0) {
SubsetList[i] = strindex;
len = 0;
}
if (ch != '\n')
SubsetArray[strindex + len++] = ch;
else {
SubsetArray[strindex + len++] = '\0';
strindex += len;
break;
}
}
}
/* now read in the domain entries */
for (i = strindex = 0; i < ndoms; i++) {
/* read in the domain identifier and transfer it to DomIdArray[] */
fscanf(fd, "%8c", domid);
DomIdArray[strindex] = domid[0];
DomIdArray[strindex + 1] = domid[1];
DomIdArray[strindex + 2] = domid[2];
DomIdArray[strindex + 3] = domid[3];
DomIdArray[strindex + 4] = domid[5];
DomIdArray[strindex + 5] = domid[7];
/* read in the subset data triples */
fscanf(fd, "%d", &n);
if (n > MAXN_SUB)
return 0;
for (j = 0; j < n; j++)
fscanf(fd, "%d %d %d", &subset[j], &grps[j], &ranks[j]);
fscanf(fd, "\n");
/* insert the entry into the hash table */
if (SubsetInsert(strindex, TableSize, n, subset, grps, ranks) < 0)
return 0;
strindex += DOMID_SIZE + 1;
}
FileClose(fd);
return 1;
} /* end LoadSubsetTable */
/* Returns the number of domains. */
Int4 LIBCALL
GetNumberOfDomains(void)
{
return NumberOfDomains;
} /* end GetNumberOfDomains */
/* Returns the number of subsets. */
Int4 LIBCALL
GetNumberOfSubsets(void)
{
return NumberOfSubsets;
} /* end GetNumberOfSubsets */
/* Returns the subset name corresponding to a subset number. */
CharPtr LIBCALL
GetSubsetName(Int4 num)
{
if ((num < 1) || (num > NumberOfSubsets))
return NULL;
return &SubsetArray[SubsetList[num - 1]];
} /* end GetSubsetName */
/* Returns the subset number corresponding to a subset name. */
Int4 LIBCALL
GetSubsetNum(Char *subname)
{
Int4 i;
for (i = 0; i < NumberOfSubsets; i++)
if (strcmp(subname, &SubsetArray[SubsetList[i]]) == 0)
return i + 1;
return 0;
} /* end GetSubsetNum */
/* This routine returns 0 if the given domain id does not belong to the specified subset.
* If it does belong then it returns the group (cluster) number within that subset, and
* also the rank within the cluster.
*/
Int4 LIBCALL
BelongsToSubset(Char *domid, Int4 sub, Int4 *grpnum, Int4 *grank)
{
Int4 h, i, h0, incr, cnt;
HT_NODE *htn;
h0 = HashDomId(domid, TableSize);
incr = IncrDomId(domid, TableSize);
*grpnum = *grank = 0;
for (i = cnt = 0; cnt < TableSize; i += incr, cnt++) {
h = (h0 + i) % TableSize;
if (HashTable[h].num < 0)
return 0;
if (strcmp(domid, &DomIdArray[HashTable[h].num]) == 0) {
for (htn = HashTable[h].next; htn != NULL; htn = htn->next)
if (htn->num == sub) {
*grpnum = htn->grpnum;
*grank = htn->grank;
return 1;
}
return 0;
}
}
/* if we get to here there's a problem */
return -1;
} /* end BelongsToSubset */
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