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diff clustalomega/clustal-omega-1.0.2/src/squid/gsi.c @ 1:bc707542e5de
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author | clustalomega |
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date | Thu, 21 Jul 2011 13:35:08 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clustalomega/clustal-omega-1.0.2/src/squid/gsi.c Thu Jul 21 13:35:08 2011 -0400 @@ -0,0 +1,387 @@ +/***************************************************************** + * 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. + *****************************************************************/ + +/* gsi.c + * Interfaces for GSI "generic sequence index" files. + * broken away from sqio.c and extended: SRE, Wed Aug 5 10:32:53 1998 + * + * + * GSI definition: + * 1 + <nfiles> + <nkeys> total records. + * Each record = 38 bytes. + * + * one header record : <"GSI" (32)> <nfiles (2)> <nkeys (4)> + * <nfiles> file records : <filename (32)> <fileno (2)> <fmt (4)> + * <nkeys> key records : <key (32)> <fileno (2)> <offset(4)> + * + * Matches up with my Perl scripts that create GSI files. + * + * RCS $Id: gsi.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: gsi.c,v 1.5 2001/08/04 20:15:42 eddy Exp) + */ + +#include <stdio.h> +#include <stdlib.h> +#include <string.h> +#ifndef SEEK_SET +#include <unistd.h> /* needed for poor crippled SunOS */ +#endif + +#include "squid.h" +#include "gsi.h" + + +/***************************************************************** + * GSI index file access routines + *****************************************************************/ + +/* Function: GSIOpen() + * + * Purpose: Open a GSI file. Returns the number of records in + * the file and a file pointer. Returns NULL on failure. + * The file pointer should be fclose()'d normally. + */ +GSIFILE * +GSIOpen(char *gsifile) +{ + GSIFILE *gsi; + char magic[GSI_KEYSIZE]; + + gsi = (GSIFILE *) MallocOrDie (sizeof(GSIFILE)); + if ((gsi->gsifp = fopen(gsifile, "r")) == NULL) + { free(gsi); squid_errno = SQERR_NOFILE; return NULL; } + + if (! fread(magic, sizeof(char), GSI_KEYSIZE, gsi->gsifp)) + { free(gsi); squid_errno = SQERR_NODATA; return NULL; } + if (strcmp(magic, "GSI") != 0) + { free(gsi); squid_errno = SQERR_FORMAT; return NULL; } + + if (! fread(&(gsi->nfiles), sizeof(sqd_uint16), 1, gsi->gsifp)) + { free(gsi); squid_errno = SQERR_NODATA; return NULL; } + if (! fread(&(gsi->recnum), sizeof(sqd_uint32), 1, gsi->gsifp)) + { free(gsi); squid_errno = SQERR_NODATA; return NULL; } + + gsi->nfiles = sre_ntoh16(gsi->nfiles); /* convert from network short */ + gsi->recnum = sre_ntoh32(gsi->recnum); /* convert from network long */ + + return gsi; +} + +/* Function: GSIGetRecord() + * + * Purpose: Each non-header record of a GSI index files consists + * of 38 bytes: 32 bytes of character string, a 2 byte + * short, and a 4 byte long. This function returns the + * three values. + * + * Args: gsi - open GSI index file, correctly positioned at a record + * f1 - char[32], allocated by caller (or NULL if unwanted) + * f2 - pointer to short (or NULL if unwanted) + * f3 - pointer to long (or NULL if unwanted) + * + * Return: 0 on failure and sets squid_errno. + */ +int +GSIGetRecord(GSIFILE *gsi, char *f1, sqd_uint16 *f2, sqd_uint32 *f3) +{ + if (f1 == NULL) fseek(gsi->gsifp, GSI_KEYSIZE, SEEK_CUR); + else if (! fread(f1, GSI_KEYSIZE, 1, gsi->gsifp)) + { squid_errno = SQERR_NODATA; return 0; } + + if (f2 == NULL) fseek(gsi->gsifp, sizeof(sqd_uint16), SEEK_CUR); + else if (! fread(f2, sizeof(sqd_uint16), 1, gsi->gsifp)) + { squid_errno = SQERR_NODATA; return 0; } + + if (f3 == NULL) fseek(gsi->gsifp, sizeof(sqd_uint32), SEEK_CUR); + else if (! fread(f3, sizeof(sqd_uint32), 1, gsi->gsifp)) + { squid_errno = SQERR_NODATA; return 0; } + + if (f2 != NULL) *f2 = sre_ntoh16(*f2); + if (f3 != NULL) *f3 = sre_ntoh32(*f3); + + return 1; +} + + +/* Function: GSIGetOffset() + * + * Purpose: From a key (sequence name), find a disk offset + * in an open general sequence index file by binary + * search. Presumably GSI indexing could be even faster + * if we used hashing. + * + * Args: gsi - GSI index file, opened by GSIOpen() + * key - name of key to retrieve indices for + * ret_seqfile - pre-alloced char[32] array for seqfile name + * ret_fmt - format of seqfile + * ret_offset - return: disk offset in seqfile. + */ +int +GSIGetOffset(GSIFILE *gsi, char *key, char *ret_seqfile, + int *ret_format, long *ret_offset) +{ + sqd_uint32 left, right, mid; + int cmp; + char name[GSI_KEYSIZE + 1]; + sqd_uint32 offset; + sqd_uint16 filenum; + sqd_uint32 fmt; + + name[GSI_KEYSIZE] = '\0'; + + left = gsi->nfiles + 1; + right = gsi->nfiles + gsi->recnum; + mid = (left + right) / 2; + fseek(gsi->gsifp, mid * GSI_RECSIZE, SEEK_SET); + + while (GSIGetRecord(gsi, name, &filenum, &offset)) + { + cmp = strcmp(name, key); + if (cmp == 0) break; /* found it! */ + else if (left >= right) return 0; /* oops, missed it; fail. */ + else if (cmp < 0) left = mid + 1; /* it's right of mid */ + else if (cmp > 0) right = mid - 1; /* it's left of mid */ + mid = (left + right) / 2; + fseek(gsi->gsifp, mid * GSI_RECSIZE, SEEK_SET); + } + + /* Using file number, look up the sequence file and format. + */ + fseek(gsi->gsifp, filenum * GSI_RECSIZE, SEEK_SET); + GSIGetRecord(gsi, ret_seqfile, NULL, &fmt); + *ret_format = (int) fmt; + *ret_offset = (long) offset; + + return 1; +} + +/* Function: GSIClose() + * + * Purpose: Close an open GSI sequence index file. + */ +void +GSIClose(GSIFILE *gsi) +{ + fclose(gsi->gsifp); + free(gsi); +} + + +/***************************************************************** + * GSI index construction routines + * SRE, Wed Nov 10 11:49:14 1999 [St. Louis] + * + * API: + * g = GSIAllocIndex(); + * + * [foreach filename, <32 char, no directory path] + * GSIAddFileToIndex(g, filename); + * filenum++; + * [foreach key, <32 char, w/ filenum 1..nfiles, w/ 32bit offset] + * GSIAddKeyToIndex(g, key, filenum, offset); + * + * GSISortIndex(g); + * GSIWriteIndex(fp, g); + * GSIFreeIndex(g); + *****************************************************************/ +struct gsiindex_s * +GSIAllocIndex(void) +{ + struct gsiindex_s *g; + + g = MallocOrDie(sizeof(struct gsiindex_s)); + g->filenames = MallocOrDie(sizeof(char *) * 10); + g->fmt = MallocOrDie(sizeof(int) * 10); + g->elems = MallocOrDie(sizeof(struct gsikey_s) * 100); + g->nfiles = 0; + g->nkeys = 0; + return g; +} +void +GSIFreeIndex(struct gsiindex_s *g) +{ + int i; + for (i = 0; i < g->nfiles; i++) free(g->filenames[i]); + free(g->filenames); + free(g->fmt); + free(g->elems); + free(g); +} +void +GSIAddFileToIndex(struct gsiindex_s *g, char *filename, int fmt) +{ + int len; + + len = strlen(filename); + if (len >= GSI_KEYSIZE) Die("File name too long to be indexed."); + g->filenames[g->nfiles] = sre_strdup(filename, len); + g->fmt[g->nfiles] = fmt; + g->nfiles++; + if (g->nfiles % 10 == 0) { + g->filenames = ReallocOrDie(g->filenames, sizeof(char *) * (g->nfiles + 10)); + g->fmt = ReallocOrDie(g->fmt, sizeof(int) * (g->nfiles + 10)); + } +} +void +GSIAddKeyToIndex(struct gsiindex_s *g, char *key, int filenum, long offset) +{ + if (strlen(key) >= GSI_KEYSIZE) Die("key too long in GSI index"); + if (filenum > SQD_UINT16_MAX) Die("too many files in GSI index"); + if (offset > SQD_UINT32_MAX) Die("offset too big in GSI index"); + + strncpy(g->elems[g->nkeys].key, key, GSI_KEYSIZE-1); + g->elems[g->nkeys].key[GSI_KEYSIZE-1] = '\0'; + g->elems[g->nkeys].filenum = (sqd_uint16) filenum; + g->elems[g->nkeys].offset = (sqd_uint32) offset; + g->nkeys++; + + if (g->nkeys % 100 == 0) + g->elems = ReallocOrDie(g->elems, sizeof(struct gsikey_s) * (g->nkeys + 100)); +} +static int +gsi_keysorter(const void *k1, const void *k2) +{ + struct gsikey_s *key1; + struct gsikey_s *key2; + key1 = (struct gsikey_s *) k1; + key2 = (struct gsikey_s *) k2; + return strcmp(key1->key, key2->key); +} +void +GSISortIndex(struct gsiindex_s *g) +{ + qsort((void *) g->elems, g->nkeys, sizeof(struct gsikey_s), gsi_keysorter); +} +void +GSIWriteIndex(FILE *fp, struct gsiindex_s *g) +{ + sqd_uint32 i; + + /* Range checking. + */ + /* AW: gcc says: comparison always false die to limited range of data type */ +#ifndef CLUSTALO + if (g->nfiles > SQD_UINT16_MAX) Die("Too many files in GSI index."); +#endif + if (g->nkeys > SQD_UINT32_MAX) Die("Too many keys in GSI index."); + + GSIWriteHeader(fp, g->nfiles, g->nkeys); + for (i = 0; i < g->nfiles; i++) + GSIWriteFileRecord(fp, g->filenames[i], i+1, g->fmt[i]); + for (i = 0; i < g->nkeys; i++) + GSIWriteKeyRecord(fp, g->elems[i].key, g->elems[i].filenum, g->elems[i].offset); +} + + + + + +/* Function: GSIWriteHeader() + * Date: SRE, Wed Aug 5 10:36:02 1998 [St. Louis] + * + * Purpose: Write the first record to an open GSI file: + * "GSI" <nfiles> <nkeys> + * + * Args: fp - open file to write to. + * nfiles - number of files indexed + * nkeys - number of keys indexed + * + * Returns: void + */ +void +GSIWriteHeader(FILE *fp, int nfiles, long nkeys) +{ + char key[GSI_KEYSIZE]; + sqd_uint16 f1; + sqd_uint32 f2; + + /* beware potential range errors! + */ + if (nfiles > SQD_UINT16_MAX) Die("GSI: nfiles out of range"); + if (nkeys > SQD_UINT32_MAX) Die("GSI: nkeys out of range"); + + f1 = (sqd_uint16) nfiles; + f2 = (sqd_uint32) nkeys; + f1 = sre_hton16(f1); + f2 = sre_hton32(f2); + strcpy(key, "GSI"); + + if (fwrite(key, 1, GSI_KEYSIZE, fp) < GSI_KEYSIZE) PANIC; + if (fwrite(&f1, 2, 1, fp) < 1) PANIC; + if (fwrite(&f2, 4, 1, fp) < 1) PANIC; +} + + +/* Function: GSIWriteFileRecord() + * Date: SRE, Wed Aug 5 10:45:51 1998 [St. Louis] + * + * Purpose: Write a file record to an open GSI file. + * + * Args: fp - open GSI file + * fname - file name (max 31 characters) + * idx - file number + * fmt - file format (e.g. kPearson, etc.) + * + * Returns: 0 on failure. 1 on success. + */ +int +GSIWriteFileRecord(FILE *fp, char *fname, int idx, int fmt) +{ + sqd_uint16 f1; + sqd_uint32 f2; + + if (strlen(fname) >= GSI_KEYSIZE) return 0; + if (idx > SQD_UINT16_MAX) Die("GSI: file index out of range"); + if (fmt > SQD_UINT32_MAX) Die("GSI: format index out of range"); + + f1 = (sqd_uint16) idx; + f2 = (sqd_uint32) fmt; + f1 = sre_hton16(f1); + f2 = sre_hton32(f2); + + if (fwrite(fname, 1, GSI_KEYSIZE, fp) < GSI_KEYSIZE) PANIC; + if (fwrite(&f1, 2, 1, fp) < 1) PANIC; + if (fwrite(&f2, 4, 1, fp) < 1) PANIC; + return 1; +} + + +/* Function: GSIWriteKeyRecord() + * Date: SRE, Wed Aug 5 10:52:30 1998 [St. Louis] + * + * Purpose: Write a key record to a GSI file. + * + * Args: fp - open GSI file for writing + * key - key (max 31 char + \0) + * fileidx - which file number to find this key in + * offset - offset for this key + * + * Returns: 1 on success, else 0. + * will fail if key >= 32 chars, for instance. + */ +int +GSIWriteKeyRecord(FILE *fp, char *key, int fileidx, long offset) +{ + sqd_uint16 f1; + sqd_uint32 f2; + + if (strlen(key) >= GSI_KEYSIZE) return 0; + if (fileidx > SQD_UINT16_MAX) Die("GSI: file index out of range"); + if (offset > SQD_UINT32_MAX) Die("GSI: offset out of range"); + + f1 = (sqd_uint16) fileidx; + f2 = (sqd_uint32) offset; + f1 = sre_hton16(f1); + f2 = sre_hton32(f2); + + if (fwrite(key, 1, GSI_KEYSIZE, fp) < GSI_KEYSIZE) PANIC; + if (fwrite(&f1, 2, 1, fp) < 1) PANIC; + if (fwrite(&f2, 4, 1, fp) < 1) PANIC; + return 1; +} +