--- /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.
+ *****************************************************************/
+#ifdef USE_GSI64
+
+/* gsi64.c
+ * Updated interfaces for GSI64 64-bit "generic sequence index" files.
+ * See gsi.c for old interfaces.
+ * This is a temporary hack! Needed for human genome project.
+ */
+
+/* 1 + <nfiles> + <nkeys> total records.
+ * Each record = 42 bytes.
+ *
+ * one header record : <"GSI64" (32)> <nfiles (2)> <nkeys (8)>
+ * <nfiles> file records : <filename (32)> <fileno (2)> <fmt (8)>
+ * <nkeys> key records : <key (32)> <fileno (2)> <offset(8)>
+ *
+ * CVS $Id: gsi64.c,v 1.2 2000/12/21 23:42:59 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 "gsi64.h"
+
+/*****************************************************************
+ * GSI64 index file access routines
+ *****************************************************************/
+
+/* Function: GSI64Open()
+ *
+ * Purpose: Open a GSI64 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.
+ */
+GSI64FILE *
+GSI64Open(char *gsifile)
+{
+ GSI64FILE *gsi;
+ char magic[GSI64_KEYSIZE];
+
+ gsi = (GSI64FILE *) MallocOrDie (sizeof(GSI64FILE));
+ if ((gsi->gsifp = fopen(gsifile, "r")) == NULL)
+ { free(gsi); squid_errno = SQERR_NOFILE; return NULL; }
+
+ if (! fread(magic, sizeof(char), GSI64_KEYSIZE, gsi->gsifp))
+ { free(gsi); squid_errno = SQERR_NODATA; return NULL; }
+ if (strcmp(magic, "GSI64") != 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_uint64), 1, gsi->gsifp))
+ { free(gsi); squid_errno = SQERR_NODATA; return NULL; }
+
+#if 0 /* HACK! we don't byteswap */
+ gsi->nfiles = sre_ntohs(gsi->nfiles); /* convert from network short */
+ gsi->recnum = sre_ntohl(gsi->recnum); /* convert from network long */
+#endif
+
+ return gsi;
+}
+
+/* Function: GSI64GetRecord()
+ *
+ * Purpose: Each non-header record of a GSI64 index file consists
+ * of 42 bytes: 32 bytes of character string, a 2 byte
+ * short, and an 8 byte long long. This function returns the
+ * three values.
+ *
+ * Args: gsi - open GSI64 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 long (or NULL if unwanted)
+ *
+ * Return: 0 on failure and sets squid_errno.
+ */
+int
+GSI64GetRecord(GSI64FILE *gsi, char *f1, sqd_uint16 *f2, sqd_uint64 *f3)
+{
+ if (f1 == NULL) fseek64(gsi->gsifp, GSI64_KEYSIZE, SEEK_CUR);
+ else if (! fread(f1, GSI64_KEYSIZE, 1, gsi->gsifp))
+ { squid_errno = SQERR_NODATA; return 0; }
+
+ if (f2 == NULL) fseek64(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) fseek64(gsi->gsifp, sizeof(sqd_uint64), SEEK_CUR);
+ else if (! fread(f3, sizeof(sqd_uint64), 1, gsi->gsifp))
+ { squid_errno = SQERR_NODATA; return 0; }
+
+#if 0 /* no byteswap yet! HACK! */
+ if (f2 != NULL) *f2 = sre_ntohs(*f2);
+ if (f3 != NULL) *f3 = sre_ntohl(*f3);
+#endif
+
+ return 1;
+}
+
+
+/* Function: GSI64GetOffset()
+ *
+ * Purpose: From a key (sequence name), find a disk offset
+ * in an open general sequence index file by binary
+ * search. Presumably GSI64 indexing could be even faster
+ * if we used hashing.
+ *
+ * Args: gsi - GSI64 index file, opened by GSI64Open()
+ * 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
+GSI64GetOffset(GSI64FILE *gsi, char *key, char *ret_seqfile,
+ int *ret_format, long long *ret_offset)
+{
+ sqd_uint64 left, right, mid;
+ int cmp;
+ char name[GSI64_KEYSIZE + 1];
+ sqd_uint64 offset;
+ sqd_uint16 filenum;
+ sqd_uint64 fmt;
+
+ name[GSI64_KEYSIZE] = '\0';
+
+ left = gsi->nfiles + 1;
+ right = gsi->nfiles + gsi->recnum;
+ mid = (left + right) / 2;
+ fseek64(gsi->gsifp, mid * GSI64_RECSIZE, SEEK_SET);
+
+ while (GSI64GetRecord(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;
+ fseek64(gsi->gsifp, mid * GSI64_RECSIZE, SEEK_SET);
+ }
+
+ /* Using file number, look up the sequence file and format.
+ */
+ fseek64(gsi->gsifp, filenum * GSI64_RECSIZE, SEEK_SET);
+ GSI64GetRecord(gsi, ret_seqfile, NULL, &fmt);
+ *ret_format = (int) fmt;
+ *ret_offset = (long long) offset;
+
+ return 1;
+}
+
+/* Function: GSI64Close()
+ *
+ * Purpose: Close an open GSI64 sequence index file.
+ */
+void
+GSI64Close(GSI64FILE *gsi)
+{
+ fclose(gsi->gsifp);
+ free(gsi);
+}
+
+
+/*****************************************************************
+ * GSI64 index construction routines
+ * SRE, Wed Nov 10 11:49:14 1999 [St. Louis]
+ *
+ * API:
+ * g = GSI64AllocIndex();
+ *
+ * [foreach filename, <32 char, no directory path]
+ * GSI64AddFileToIndex(g, filename);
+ * filenum++;
+ * [foreach key, <32 char, w/ filenum 1..nfiles, w/ 64bit offset]
+ * GSI64AddKeyToIndex(g, key, filenum, offset);
+ *
+ * GSI64SortIndex(g);
+ * GSI64WriteIndex(fp, g);
+ * GSI64FreeIndex(g);
+ *****************************************************************/
+struct gsi64index_s *
+GSI64AllocIndex(void)
+{
+ struct gsi64index_s *g;
+
+ g = MallocOrDie(sizeof(struct gsi64index_s));
+ g->filenames = MallocOrDie(sizeof(char *) * 10);
+ g->fmt = MallocOrDie(sizeof(int) * 10);
+ g->elems = MallocOrDie(sizeof(struct gsi64key_s) * 100);
+ g->nfiles = 0;
+ g->nkeys = 0;
+ return g;
+}
+void
+GSI64FreeIndex(struct gsi64index_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
+GSI64AddFileToIndex(struct gsi64index_s *g, char *filename, int fmt)
+{
+ int len;
+
+ len = strlen(filename);
+ if (len >= GSI64_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
+GSI64AddKeyToIndex(struct gsi64index_s *g, char *key, int filenum, long long offset)
+{
+ if (strlen(key) >= GSI64_KEYSIZE) Die("key too long in GSI64 index");
+ if (filenum > SQD_UINT16_MAX) Die("too many files in GSI64 index");
+ if (offset > SQD_UINT64_MAX) Die("offset too big in GSI64 index");
+
+ strncpy(g->elems[g->nkeys].key, key, GSI64_KEYSIZE-1);
+ g->elems[g->nkeys].key[GSI64_KEYSIZE-1] = '\0';
+ g->elems[g->nkeys].filenum = (sqd_uint16) filenum;
+ g->elems[g->nkeys].offset = (sqd_uint64) offset;
+ g->nkeys++;
+
+ if (g->nkeys % 100 == 0)
+ g->elems = ReallocOrDie(g->elems, sizeof(struct gsi64key_s) * (g->nkeys + 100));
+}
+static int
+gsi_keysorter(const void *k1, const void *k2)
+{
+ struct gsi64key_s *key1;
+ struct gsi64key_s *key2;
+ key1 = (struct gsi64key_s *) k1;
+ key2 = (struct gsi64key_s *) k2;
+ return strcmp(key1->key, key2->key);
+}
+void
+GSI64SortIndex(struct gsi64index_s *g)
+{
+ qsort((void *) g->elems, g->nkeys, sizeof(struct gsi64key_s), gsi_keysorter);
+}
+void
+GSI64WriteIndex(FILE *fp, struct gsi64index_s *g)
+{
+ sqd_uint16 i;
+ sqd_uint64 j;
+
+ /* Range checking.
+ */
+ if (g->nfiles > SQD_UINT16_MAX) Die("Too many files in GSI64 index.");
+ if (g->nkeys > SQD_UINT64_MAX) Die("Too many keys in GSI64 index.");
+
+ GSI64WriteHeader(fp, g->nfiles, g->nkeys);
+ for (i = 0; i < g->nfiles; i++)
+ GSI64WriteFileRecord(fp, g->filenames[i], i+1, g->fmt[i]);
+ for (j = 0; j < g->nkeys; j++)
+ GSI64WriteKeyRecord(fp, g->elems[j].key, g->elems[j].filenum, g->elems[j].offset);
+}
+
+
+
+
+
+/* Function: GSI64WriteHeader()
+ * Date: SRE, Wed Aug 5 10:36:02 1998 [St. Louis]
+ *
+ * Purpose: Write the first record to an open GSI64 file:
+ * "GSI64" <nfiles> <nkeys>
+ *
+ * Args: fp - open file to write to.
+ * nfiles - number of files indexed
+ * nkeys - number of keys indexed
+ *
+ * Returns: void
+ */
+void
+GSI64WriteHeader(FILE *fp, int nfiles, long long nkeys)
+{
+ char key[GSI64_KEYSIZE];
+ sqd_uint16 f1;
+ sqd_uint64 f2;
+
+ /* beware potential range errors!
+ */
+ if (nfiles > SQD_UINT16_MAX) Die("GSI64: nfiles out of range");
+ if (nkeys > SQD_UINT64_MAX) Die("GSI64: nkeys out of range");
+
+ f1 = (sqd_uint16) nfiles;
+ f2 = (sqd_uint64) nkeys;
+#if 0 /* HACK no byteswap */
+ f1 = sre_htons(f1);
+ f2 = sre_htonl(f2);
+#endif
+ strcpy(key, "GSI64");
+
+ if (fwrite(key, 1, GSI64_KEYSIZE, fp) < GSI64_KEYSIZE) PANIC;
+ if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
+ if (fwrite(&f2, 8, 1, fp) < 1) PANIC;
+}
+
+
+/* Function: GSI64WriteFileRecord()
+ * Date: SRE, Wed Aug 5 10:45:51 1998 [St. Louis]
+ *
+ * Purpose: Write a file record to an open GSI64 file.
+ *
+ * Args: fp - open GSI64 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
+GSI64WriteFileRecord(FILE *fp, char *fname, int idx, int fmt)
+{
+ sqd_uint16 f1;
+ sqd_uint64 f2;
+
+ if (strlen(fname) >= GSI64_KEYSIZE) return 0;
+ if (idx > SQD_UINT16_MAX) Die("GSI64: file index out of range");
+ if (fmt > SQD_UINT64_MAX) Die("GSI64: format index out of range");
+
+ f1 = (sqd_uint16) idx;
+ f2 = (sqd_uint64) fmt;
+#if 0 /* hack : no byteswap */
+ f1 = sre_htons(f1);
+ f2 = sre_htonl(f2);
+#endif
+
+ if (fwrite(fname, 1, GSI64_KEYSIZE, fp) < GSI64_KEYSIZE) PANIC;
+ if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
+ if (fwrite(&f2, 8, 1, fp) < 1) PANIC;
+ return 1;
+}
+
+
+/* Function: GSI64WriteKeyRecord()
+ * Date: SRE, Wed Aug 5 10:52:30 1998 [St. Louis]
+ *
+ * Purpose: Write a key record to a GSI64 file.
+ *
+ * Args: fp - open GSI64 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
+GSI64WriteKeyRecord(FILE *fp, char *key, int fileidx, long long offset)
+{
+ sqd_uint16 f1;
+ sqd_uint64 f2;
+
+ if (strlen(key) >= GSI64_KEYSIZE) return 0;
+ if (fileidx > SQD_UINT16_MAX) Die("GSI64: file index out of range");
+ if (offset > SQD_UINT64_MAX) Die("GSI64: offset out of range");
+
+ f1 = (sqd_uint16) fileidx;
+ f2 = (sqd_uint64) offset;
+#if 0 /* HACK! */
+ f1 = sre_htons(f1);
+ f2 = sre_htonl(f2);
+#endif
+
+ if (fwrite(key, 1, GSI64_KEYSIZE, fp) < GSI64_KEYSIZE) PANIC;
+ if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
+ if (fwrite(&f2, 8, 1, fp) < 1) PANIC;
+ return 1;
+}
+
+#endif /*USE_GSI64 */
git://source.jalview.org / jabaws.git / blobdiff