misc.c

来自「这是一个基于HMM 模型的生物多序列比对算法的linux实现版本。hmmer」· C语言 代码 · 共 178 行

/************************************************************
 * HMMER - Biological sequence analysis with profile HMMs
 * Copyright (C) 1992-2003 Washington University School of Medicine
 * All Rights Reserved
 * 
 *     This source code is distributed under the terms of the
 *     GNU General Public License. See the files COPYING and LICENSE
 *     for details.
 ************************************************************/

/* misc.c
 * SRE, Thu Jul 15 18:49:19 1993
 * 
 * Functions that I don't know quite where to put yet.
 */

#include "config.h"
#include "squidconf.h"

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <float.h>
#include <limits.h>

#include "squid.h"
#include "structs.h"


/* Function: HMMERBanner()
 * Date:     SRE, Sun Jun 20 17:19:41 1999 [Graeme's kitchen]
 *
 * Purpose:  Print a package version and copyright banner.
 *           Used by all the main()'s.
 *           
 *    Expects to be able to pick up defined preprocessor variables:
 *    variable          example
 *    --------           --------------  
 *    PACKAGE_NAME      "HMMER"
 *    PACKAGE_VERSION   "2.0.42"
 *    PACKAGE_DATE      "April 1999"
 *    PACKAGE_COPYRIGHT "Copyright (C) 1992-1999 Washington University School of Medicine"
 *    PACKAGE_LICENSE   "Freely distributed under the GNU General Public License (GPL)."
 *           
 *    This gives us a general mechanism to update release information
 *    without changing multiple points in the code.
 * 
 * Args:     fp     - where to print it
 *           banner - one-line program description, e.g.:
 *                    "foobar - make bars from foo with elan" 
 * Returns:  (void)
 */
void
HMMERBanner(FILE *fp, char *banner)
{
  fprintf(fp, "%s\n", banner);
  fprintf(fp, "%s %s (%s)\n", PACKAGE_NAME, PACKAGE_VERSION, PACKAGE_DATE);
  fprintf(fp, "%s\n", PACKAGE_COPYRIGHT);
  fprintf(fp, "%s\n", PACKAGE_LICENSE);
  fprintf(fp, "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n");
}



/* Function: Getword()
 * 
 * Purpose:  little function used by ReadPrior() and ReadHMM() to parse
 *           next valid field out of an open file, ignoring
 *           comments. '#' marks the beginning of a comment.
 *
 * Arg:      fp   - open file for reading
 *           type - sqdARG_INT, sqdARG_FLOAT, or sqdARG_STRING from squid.h
 */
char *
Getword(FILE *fp, int type)
{
  static char buffer[512];
  static char *sptr = NULL;
  
  if (sptr != NULL) sptr = strtok(NULL, " \t\n");

  while (sptr == NULL)
    {
      if ((sptr = fgets(buffer, 512, fp)) == NULL) return NULL;
      if ((sptr = strchr(buffer, '#')) != NULL) *sptr = '\0';
      sptr = strtok(buffer, " \t\n");
    }

  switch (type) {
  case sqdARG_STRING: 
    if (strlen(sptr) == 0) { 
      Warn("Parse failed: expected string, got nothing"); 
      sptr = NULL; 
    }
    break;
  case sqdARG_INT:    
    if (!IsInt(sptr)) {
      Warn("Parse failed: expected integer, got %s", sptr);
      sptr = NULL;
    }
    break;
  case sqdARG_FLOAT:
    if (!IsReal(sptr)) {
      Warn("Parse failed: expected real value, got %s", sptr); 
      sptr = NULL;
    }
    break;
  }

  return sptr;
}


/* Function: Getline()
 * 
 * Purpose:  Get the next non-blank, non-comment line from an open file.
 *           A comment line has '#' as the first non-whitespace character.
 *           Returns NULL if no line is found. 
 *           Syntax is the same as fgets().
 *           
 * Args:     s  - allocated storage for line
 *           n  - number of characters allocated for s
 *           fp - open FILE *
 *           
 * Return:   Either s, or NULL if no new line is found.
 */        
char * 
Getline(char *s, int n, FILE *fp)
{
  char *first;

  do {
    if (fgets(s, n, fp) == NULL) return NULL;
    first = s; while (isspace((int) (*first))) first++;
  } while (*first == '#' || *first == '\0');
  return s;
}


/* Function: SetAutocuts()
 * Date:     SRE, Thu Jun  8 08:19:46 2000 [TW721 over Ireland]
 *
 * Purpose:  Set score thresholds using the GA, TC, or NC information
 *           in an HMM.
 *
 * Args:     thresh - score threshold structure. autocut must be set
 *                    properly (CUT_GA, CUT_NC, or CUT_TC).
 *           hmm    - HMM containing appropriate score cutoff info
 *
 * Returns:  1 on success.
 *           0 if HMM does not have the score cutoffs available -- caller
 *             will have to decide on a fallback plan.
 *           Has no effect (and returns success) if autocut is
 *           CUT_NONE.
 */
int
SetAutocuts(struct threshold_s *thresh, struct plan7_s *hmm)
{
  if (thresh->autocut == CUT_GA) {
    if (! (hmm->flags & PLAN7_GA)) return 0;
    thresh->globT = hmm->ga1;
    thresh->domT  = hmm->ga2;
    thresh->globE = thresh->domE = FLT_MAX;
  } else if (thresh->autocut == CUT_NC) {
    if (! (hmm->flags & PLAN7_NC)) return 0;
    thresh->globT = hmm->nc1;
    thresh->domT  = hmm->nc2;
    thresh->globE = thresh->domE = FLT_MAX;
  } else if (thresh->autocut == CUT_TC) {
    if (! (hmm->flags & PLAN7_TC)) return 0;
    thresh->globT = hmm->tc1;
    thresh->domT  = hmm->tc2;
    thresh->globE = thresh->domE = FLT_MAX;
  }
  return 1;
}