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contrib/GeneFinder/genefinder/gfcode.c  view on Meta::CPAN

static void lettsToNums (Sequence *sequence, GfTable *table) ;
static void countsToFreqs (GfTable *table, int selfSample) ;
static void cleanNucCounts (GfTable *table) ;
static void makeNucFreqs (GfTable *table, int selfSample) ;
static float tPower (float x) ;
static float lRatio (float nCounts, float nTotal, int selfSample) ;
static void makeClassNucFreqs (GfTable *table, int selfSample) ;
static void logDiffs (GfTable *table1, GfTable *table2) ;
static GfTable *readTableFile (char *tableFile, int initial, int selfSample) ;
static GfTable *initTable (void) ;
static void expandTable (GfTable *table) ;
static int **allocIntMat (GfTable *table) ;
static float **allocFloatMat (GfTable *table) ;
static int *makeConvTable (void) ;
static void aceFeatures (Sequence *seq, GfTableVec *tVec, float *fp) ;
static int aceSites (Sequence *sequence, GfTable *table, float cutoff, int type) ;
static void aceMaxSegs (double *cumVec, int start, int end) ;
 
/*****************************************************/

static void lettsToNums (Sequence *sequence, GfTable *table)

contrib/GeneFinder/genefinder/gfcode.c  view on Meta::CPAN

		 tableFile, string);
#else
      fprintf(stderr, "ERROR in tableFile %s: \"%s\" unknown field\n",
	      tableFile, string);
      exit(1);
#endif
    }
  };
  table->classes[iclass][0] = 0;
  table->numClasses = iclass;
  expandTable(table);

  if (!initial) {
    for (i = 0; i < table->numRows; i++)
      for (j = 0; j < table->numCols; j++) {
	d = fscanf(fp, "%d", &table->nucCounts[i][j]);
	if (!d || d == EOF) {
#ifdef ACEDB
	  messcrash ("scoreTable %s incomplete", tableFile);
#else
	  fprintf(stderr, "scoreTable %s incomplete", tableFile);

contrib/GeneFinder/genefinder/gfcode.c  view on Meta::CPAN

  table->jump = 1; /*default jump size: for ordinary tables */
  table->numForced = 0; /*default is no positions forced */
  strcpy(table->refSeqs,"all"); /*default reference sequences*/
  strcpy(table->freqType,"within"); 
  strcpy(table->classDef,"unique"); /*default frequency calculations:
       single class, frequencies are relative to it */
  return table;
}

/* fill in additional (derivative) values in the table structure */
static void expandTable (GfTable *table)
{
  int modNum, i;

  table->convTable = makeConvTable();
  table->numCols = (table->endOff - table->startOff - table->numSymbs + 1)/table->jump + 1;
  modNum = 1;
  for (i = 1; i < table->numSymbs; i++) modNum *= table->maxSymb;
  table->modNum = modNum;
  table->numRows = modNum * table->maxSymb;
  if (strcmp(table->classDef,"defined")){