--- /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.
+ *****************************************************************/
+
+/* 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;
+}
+
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