#include "dnautil.h"Include dependency graph for codebias.h:
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Data Structures | |
| struct | codonBias |
Functions | |
| codonBias * | codonLoadBias (char *fileName) |
| int | codonFindFrame (DNA *dna, int dnaSize, struct codonBias *forBias) |
Definition at line 100 of file codebias.c.
References codonBias::mark0, codonBias::mark1, ntVal, and unN().
00103 { 00104 double logOneFourth = log(0.25); 00105 double logProbs[3]; 00106 int frame; 00107 int dnaIx; 00108 double logP; 00109 double bestLogP = -0x6fffffff; 00110 int bestFrame = -1; 00111 int lastDnaStart = dnaSize-3; 00112 DNA *d; 00113 int codon = 0, lastCodon; 00114 00115 unN(dna, dnaSize); 00116 for (frame=0; frame<3; ++frame) 00117 { 00118 /* Partial first codon just gets even background score. */ 00119 logP = frame*logOneFourth; 00120 /* 1st order model on first full codon. */ 00121 if (frame <= lastDnaStart) 00122 { 00123 d = dna+frame; 00124 codon = (ntVal[(int)d[0]]<<4) + (ntVal[(int)d[1]]<<2) + ntVal[(int)d[2]]; 00125 logP += forBias->mark0[codon]; 00126 } 00127 /* 2nd order model on subsequent full codons. */ 00128 for (dnaIx = frame+3; dnaIx <= lastDnaStart; dnaIx += 3) 00129 { 00130 lastCodon = codon; 00131 d = dna+dnaIx; 00132 codon = (ntVal[(int)d[0]]<<4) + (ntVal[(int)d[1]]<<2) + ntVal[(int)d[2]]; 00133 logP += forBias->mark1[lastCodon][codon]; 00134 } 00135 /* Partial last codon gets even background score. */ 00136 logP += (dnaSize-dnaIx)*logOneFourth; 00137 logProbs[frame] = logP; 00138 if (logP > bestLogP) 00139 { 00140 bestLogP = logP; 00141 bestFrame = frame; 00142 } 00143 } 00144 return bestFrame; 00145 }
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| struct codonBias* codonLoadBias | ( | char * | fileName | ) | [read] |
Definition at line 14 of file codebias.c.
References AllocVar, chopLine, errAbort(), FALSE, codonBias::mark0, codonBias::mark1, mustOpen(), sameString, scaledLog(), startsWith(), and TRUE.
00017 { 00018 struct codonBias *cb; 00019 char line[1024]; 00020 int lineCount = 0; 00021 char *words[128]; 00022 int wordCount; 00023 int i = 0, j = 0; 00024 int skip = 0; 00025 boolean getMark0 = FALSE; 00026 boolean getMark1 = FALSE; 00027 FILE *f = mustOpen(fileName, "r"); 00028 int val; 00029 00030 AllocVar(cb); 00031 while (fgets(line, sizeof(line), f) ) 00032 { 00033 ++lineCount; 00034 if (skip) 00035 { 00036 skip -= 1; 00037 continue; 00038 } 00039 if (getMark1) 00040 { 00041 wordCount = chopLine(line, words); 00042 if (wordCount != 65) 00043 errAbort("Bad line %d of %s\n", lineCount, fileName); 00044 for (j=0; j<64; ++j) 00045 { 00046 val = atoi(words[j+1]); 00047 if (val == 0) 00048 cb->mark1[i][j] = scaledLog(1.0E-20); 00049 else 00050 cb->mark1[i][j] = scaledLog(0.001*val); 00051 } 00052 if ((i += 1) == 64) 00053 getMark1 = FALSE; 00054 } 00055 else if (getMark0) 00056 { 00057 wordCount = chopLine(line, words); 00058 if (wordCount != 64) 00059 errAbort("Bad line %d of %s\n", lineCount, fileName); 00060 for (j=0; j<64; ++j) 00061 { 00062 val = atoi(words[j]); 00063 if (val == 0) 00064 cb->mark0[j] = scaledLog(1.0E-20); 00065 else 00066 cb->mark0[j] = scaledLog(0.001*val); 00067 } 00068 getMark0 = FALSE; 00069 } 00070 else if (startsWith("Markov", line)) 00071 { 00072 wordCount = chopLine(line, words); 00073 if (wordCount != 2) 00074 errAbort("Bad line %d of %s\n", lineCount, fileName); 00075 if (sameString(words[1], "0")) 00076 getMark0 = TRUE; 00077 else if (sameString(words[1], "1")) 00078 getMark1 = TRUE; 00079 else 00080 errAbort("Bad line %d of %s\n", lineCount, fileName); 00081 skip = 3; 00082 } 00083 } 00084 fclose(f); 00085 return cb; 00086 }
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1.5.2