NCBI C Toolkit Cross Reference

C/desktop/aacomp.c

  1 #include <objres.h>
  2 #include <objseq.h>
  3 #include <seqport.h>
  4 #include <aacomp.h>
  5 
  6 /* defines */
  7 #define F7   7
  8 #define F24 24
  9 #define F42 42
 10 #define PI  3.14159
 11 
 12 /* functions - internal */
 13 
 14 static FloatHiPtr AAC (SeqPortPtr spp, Int4 start, Int4 end,
 15                        Int4 numval, Int4 window,
 16                        FloatHiPtr scr, CharPtr res)
 17 {
 18   Int4        i, n, col;
 19   Int4        stop;
 20   Char        aa;
 21   Boolean     flagMatch;
 22   FloatHi     temp, fmin = 0.0, fmax = 0.0, frange;
 23   FloatHiPtr  frealheadptr, fheadptr;
 24   FloatHiPtr  fptr;
 25 
 26   fptr = (FloatHiPtr) MemNew ((sizeof (FloatHi)) * numval);
 27   frealheadptr = fptr;
 28   for (i = start; i < end+1; i++)
 29     *fptr++ = 0.0;
 30   fptr = frealheadptr;
 31 
 32   for (i = 0; i < window/2; i++)
 33     fptr++;
 34   fheadptr = fptr;
 35   stop = end + 1 - window + 1;
 36   for (i = start; i < stop; i++)
 37   {
 38     temp = 0;
 39     SeqPortSeek (spp, i, SEEK_SET);
 40     for (col = 0; col < window; col++)
 41     {
 42       aa = SeqPortGetResidue (spp);
 43       flagMatch = FALSE;
 44       n = 0;
 45       while (res[n] != '\0')
 46       {
 47         if (aa == res[n])
 48         {
 49           flagMatch = TRUE;
 50           break;
 51         }
 52         n++;
 53       }
 54       if (flagMatch)
 55         temp += scr[n];
 56     }
 57     temp /= window;
 58     *fptr = temp;
 59     fptr++;
 60   }
 61   fptr = fheadptr;
 62   for (i = start; i < stop; i++)
 63   {
 64     if (*fptr > fmax)
 65       fmax = *fptr;
 66     fptr++;
 67   }
 68   fptr = fheadptr;
 69   for (i = start; i < stop; i++)
 70   {
 71     if (*fptr < fmin)
 72       fmin = *fptr;
 73     fptr++;
 74   }
 75   frange = fmax-fmin;
 76   fptr = fheadptr;
 77   for (i = start; i < stop; i++)
 78   {
 79     *fptr = (*fptr - fmin)/frange*100;
 80     fptr++;
 81   }
 82 
 83   return frealheadptr;
 84 }
 85 
 86 static SeqGraphPtr AACGraph (SeqPortPtr spp, Int4 start, Int4 end, Int4 window,
 87                              FloatHiPtr scr, CharPtr res)
 88 {
 89   SeqGraphPtr  sgp;
 90   Int4         gwidth = 500;
 91 
 92   if ((sgp = SeqGraphNew ()) != NULL)
 93   {
 94 /* type and number of values and compression */
 95     sgp->numval = end + 1;
 96     sgp->compr = (Int4) (sgp->numval / gwidth);
 97     if ((sgp->numval%gwidth) != 0)
 98       sgp->compr += 1;
 99 /* graph type */
100     sgp->flags[2] = 1;
101     sgp->values = (Pointer) MemNew ((sizeof (FloatHi)) * sgp->numval);
102 /* min/max */
103     sgp->max.realvalue = 100.0;
104     sgp->min.realvalue = 0.0;
105     sgp->axis.realvalue = 0.0;
106 /* scaling */
107     sgp->flags[1] = 1;
108     sgp->a = 2;
109     sgp->b = 0;
110 /* do it */
111     AAC (spp, start, end, end+1, window, scr, res);
112   }
113   return sgp;
114 }
115 
116 /*
117  this stores a score for each of 24 resides
118   20 amino acids
119    2 ambiguous amino acids (ASX GLX)
120    1 unknown amino acid (the average score of the 20 generally)
121    1 stop codon (currently also the average score of the 20)
122  the scoring table should have the scores in a column
123  in order of the residues stored in static Char c[]
124 
125  the caller must pass pointers to arrays that can hold
126  the 24 residues (res) and scores (scr)
127 
128  a successful, tho not necessarily correct, read will return 24
129 */
130 
131 extern Int4 ReadAAC (CharPtr filename, FloatHiPtr scr, CharPtr res)
132 {
133   Int2     val, count;
134   Int4     type;
135   long int ltype;
136   FloatHi  score;
137   Char     buf[PATH_MAX], buff[PATH_MAX];
138   CharPtr  bptr;
139   FILE     *fio;
140 
141   static Char c[] = {'A','B','C','D','E','F','G','H','I','K','L','M',
142                      'N','P','Q','R','S','T','V','W','X','Y','Z','*'};
143 
144   if (!FindPath ("ncbi", "ncbi", "data", buf, sizeof (buf)))
145     return 0;
146   FileBuildPath (buf, NULL, filename);
147   if ((fio = FileOpen (buf, "r")) == NULL)
148   {
149     if ((fio = FileOpen (filename, "r")) == NULL)
150     {
151       return 0;
152     }
153   }
154 
155   val = 0;
156   type = -1;
157   while ((FileGets (buff, sizeof (buff), fio)) != NULL)
158   {
159     if (buff[0] == ';')
160       continue;
161     if (type == -1)
162     {
163       sscanf (buff, "%ld", &ltype);
164       type = (Int4) ltype;
165       if (type != 1)
166       {
167         FileClose (fio);
168         return 0;
169       }
170       FileGets (buff, sizeof (buff), fio);
171       continue;
172     }
173 
174     res[val] = c[val];
175     bptr = buff;
176 
177     sscanf (bptr, "%lf", &score);
178     scr[val] = score;
179 
180     val++;
181     if (val == F24)
182       break;
183   }
184   count = val;
185 
186   FileClose (fio);
187   return (Int4) count;
188 }
189 
190 /* functions - external */
191 
192 extern FloatHiPtr AAComposition (SeqPortPtr spp,
193                                  Int4 start, Int4 end, Int4 numval,
194                                  FloatHiPtr scr, CharPtr res, Int4 window)
195 {
196   FloatHiPtr   fptr;
197 
198   fptr = AAC (spp, start, end, numval, window, scr, res);
199   return fptr;
200 }
201 
202
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