1 | /* #include <malloc.h> */ |
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2 | #include <stdio.h> |
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3 | #include <stdlib.h> |
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4 | #include <string.h> |
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5 | |
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6 | #define TRUE 1 |
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7 | #define FALSE 0 |
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8 | #define MAX(a,b) ((a)>(b)?(a):(b)) |
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9 | #define MIN(a,b) ((a)<(b)?(a):(b)) |
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10 | |
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11 | struct data_format |
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12 | { |
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13 | int length; |
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14 | char *nuc; |
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15 | int offset; |
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16 | char name[64]; |
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17 | char type; |
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18 | }; |
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19 | |
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20 | |
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21 | void ErrorOut(code,string) |
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22 | int code; |
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23 | char *string; |
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24 | { |
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25 | if (code == 0) |
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26 | { |
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27 | fprintf(stderr,"Error:%s\n",string); |
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28 | exit(1); |
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29 | } |
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30 | } |
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31 | |
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32 | char *Calloc2(count,size) |
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33 | int count,size; |
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34 | { |
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35 | char *temp; |
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36 | |
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37 | temp = (char*)calloc(count,size); |
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38 | if(temp == NULL) |
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39 | { |
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40 | fprintf(stdout,"Error in Calloc\n"); |
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41 | exit(-1); |
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42 | } |
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43 | else |
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44 | return(temp); |
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45 | } |
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46 | |
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47 | char *Realloc(block,size) |
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48 | char *block; |
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49 | int size; |
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50 | { |
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51 | char *temp; |
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52 | temp =(char*)realloc(block,size); |
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53 | if(temp == NULL) |
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54 | { |
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55 | fprintf(stdout,"Error in Calloc\n"); |
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56 | exit(-1); |
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57 | } |
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58 | else |
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59 | return(temp); |
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60 | } |
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61 | |
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62 | |
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63 | |
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64 | int ReadFlat(file,align,maxseqs) |
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65 | FILE *file; |
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66 | struct data_format align[]; |
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67 | int maxseqs; |
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68 | { |
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69 | int j,len=0, count=-1,offset; |
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70 | unsigned maxlen = 1024; |
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71 | char Inline[1025]; |
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72 | |
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73 | if(file == NULL) |
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74 | ErrorOut(0, "Cannot open data file"); |
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75 | |
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76 | for(;fgets(Inline,1024,file) != NULL;) |
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77 | { |
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78 | Inline[strlen(Inline)-1] = '\0'; |
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79 | switch(Inline[0]) |
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80 | { |
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81 | case '>': |
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82 | case '#': |
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83 | case '%': |
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84 | case '"': |
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85 | case '@': |
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86 | offset = 0; |
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87 | { |
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88 | int InlineLen=strlen(Inline); |
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89 | for(j=0;j<InlineLen;j++) |
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90 | { |
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91 | if(Inline[j] == '(') |
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92 | { |
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93 | sscanf((char*) |
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94 | (Inline+j+1),"%d", |
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95 | &offset); |
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96 | Inline[j] = '\0'; |
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97 | } |
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98 | } |
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99 | } |
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100 | |
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101 | if(count != -1) |
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102 | { |
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103 | align[count].length = len; |
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104 | align[count].nuc[len] = '\0'; |
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105 | maxlen = len; |
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106 | } |
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107 | |
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108 | count++; |
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109 | if(count > maxseqs) |
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110 | ErrorOut(0, "Sorry, alignment is too large"); |
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111 | |
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112 | align[count].nuc = Calloc2(maxlen,sizeof(char)); |
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113 | align[count].type = Inline[0]; |
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114 | align[count].offset = offset; |
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115 | if( align[count].nuc == NULL) |
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116 | ErrorOut(0, "Calloc problem"); |
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117 | |
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118 | sscanf((char*)(Inline+1),"%s", |
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119 | align[count].name); |
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120 | len = 0; |
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121 | break; |
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122 | default: |
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123 | if(len+strlen(Inline) > maxlen) |
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124 | { |
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125 | maxlen = (maxlen+strlen(Inline))*2; |
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126 | align[count].nuc = |
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127 | Realloc(align[count].nuc, maxlen); |
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128 | } |
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129 | { |
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130 | int InlineLen=strlen(Inline); |
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131 | for(j=0;j<InlineLen;j++) |
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132 | align[count].nuc[j+len] = Inline[j]; |
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133 | } |
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134 | len += strlen(Inline); |
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135 | break; |
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136 | } |
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137 | } |
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138 | if(count == -1) exit(1); |
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139 | |
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140 | align[count].length = len; |
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141 | align[count].nuc[len] = '\0'; |
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142 | return(++count); |
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143 | } |
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