2 |
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#include <stdlib.h> |
3 |
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#include <string.h> |
4 |
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|
5 |
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#define STR_BUFFER_SIZE 500 |
6 |
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|
7 |
< |
char *program_name; /*the name of the program */ |
7 |
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// ******************************************************* |
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// Uncomment the following two tyedefs to support multiple |
9 |
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// input files |
10 |
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// ******************************************************* |
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|
12 |
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typedef struct{ |
13 |
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char fileName[STR_BUFFER_SIZE]; |
14 |
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FILE* filePtr; |
15 |
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} fileStruct; |
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|
17 |
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typedef struct linkedNameTag { |
18 |
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char name[STR_BUFFER_SIZE]; |
19 |
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struct linkedNameTag* next; |
20 |
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} linkedName; |
21 |
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|
22 |
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// ******************************************************* |
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// end multiple file support |
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// ******************************************************* |
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|
26 |
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|
27 |
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char *programName; /*the name of the program */ |
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void usage(void); |
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|
30 |
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int main(argc, argv) |
31 |
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int argc; |
32 |
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char *argv[]; |
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int main(argC, argV) |
31 |
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int argC; |
32 |
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char *argV[]; |
33 |
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{ |
34 |
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int i,j; // loop counters |
35 |
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|
36 |
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char *in_name = NULL; // name of the input file |
37 |
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char* out_prefix = NULL; // the output prefix |
38 |
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char current_flag; // used in parsing the flags |
36 |
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char* outPrefix; // the output prefix |
37 |
> |
|
38 |
> |
char* conversionCheck; |
39 |
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int conversionError; |
40 |
> |
int optionError; |
41 |
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|
42 |
> |
char currentFlag; // used in parsing the flags |
43 |
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int done = 0; // multipurpose boolean |
44 |
< |
int have_prefix; // boolean for the output prefix |
44 |
> |
int havePrefix; // boolean for the output prefix |
45 |
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|
46 |
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int flag1; |
47 |
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char flag1Arg1[STR_BUFFER_SIZE]; |
48 |
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char flag1Arg2[STR_BUFFER_SIZE]; |
49 |
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int flag2; |
50 |
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double flag2Val; |
51 |
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int flag3; |
52 |
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int rFlag; |
53 |
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int iFlag, iVal; |
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|
55 |
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// ********************************************************** |
56 |
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// to support single or multiple input files, uncomment the |
57 |
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// appropriate declarations |
58 |
+ |
// ********************************************************** |
59 |
+ |
// single: |
60 |
+ |
|
61 |
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char* inName; |
62 |
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FILE* inFile; |
63 |
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|
64 |
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// *********************************************************** |
65 |
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// multiple: |
66 |
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|
67 |
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fileStruct* inputArray; |
68 |
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linkedName* headName; |
69 |
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linkedName* currentName; |
70 |
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int nInputs; |
71 |
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|
72 |
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// end input file declarations |
73 |
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// *********************************************************** |
74 |
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|
75 |
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|
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|
77 |
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// intialize default values |
78 |
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|
79 |
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|
80 |
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// ******************************************** |
81 |
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// single input: |
82 |
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|
83 |
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inName = NULL; |
84 |
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inFile = NULL; |
85 |
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|
86 |
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// ********************************************* |
87 |
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// multiple input: |
88 |
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|
89 |
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nInputs = 0; |
90 |
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inputArray = NULL; |
91 |
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headName = NULL; |
92 |
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currentName = NULL; |
93 |
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|
94 |
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// end file initialization |
95 |
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// ********************************************** |
96 |
+ |
|
97 |
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|
98 |
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|
99 |
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outPrefix = NULL; |
100 |
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|
101 |
+ |
conversionError = 0; |
102 |
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optionError = 0; |
103 |
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|
104 |
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havePrefix = 0; |
105 |
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flag1 = 0; |
106 |
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flag2 = 0; |
107 |
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flag3 = 0; |
108 |
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rFlag = 0; |
109 |
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iFlag = 0; |
110 |
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|
111 |
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|
112 |
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iVal = 0; |
113 |
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|
114 |
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|
115 |
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|
116 |
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// here we set the name of the program need by the usage message |
117 |
< |
program_name = argv[0]; |
117 |
> |
programName = argV[0]; |
118 |
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|
119 |
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|
120 |
< |
for( i = 1; i < argc; i++){ |
120 |
> |
for( i = 1; i < argC; i++){ |
121 |
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|
122 |
< |
if(argv[i][0] =='-'){ |
122 |
> |
if(argV[i][0] =='-'){ |
123 |
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|
124 |
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// parse the option |
125 |
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|
126 |
< |
if(argv[i][1] == '-' ){ |
126 |
> |
if(argV[i][1] == '-' ){ |
127 |
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|
128 |
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// parse long word options |
129 |
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|
130 |
< |
if( !strcmp( argv[i], "--GofR" ) ){ |
131 |
< |
calcGofR = 1; |
130 |
> |
if( !strcmp( argV[i], "--flag1" ) ){ |
131 |
> |
flag1 = 1; // set flag1 to true |
132 |
> |
|
133 |
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i++; |
134 |
< |
strcpy( gofR1, argv[i] ); |
134 |
> |
strcpy( flag1Arg1, argV[i] ); |
135 |
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i++; |
136 |
< |
strcpy( gofR2, argv[i] ); |
136 |
> |
strcpy( flag1Arg2, argV[i] ); |
137 |
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} |
138 |
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|
139 |
< |
else if( !strcmp( argv[i], "--CosCorr" ) ){ |
140 |
< |
calcCosCorr = 1; |
139 |
> |
else if( !strcmp( argV[i], "--flag2" ) ){ |
140 |
> |
flag2 = 1; // set the flag2 to true; |
141 |
> |
|
142 |
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i++; |
143 |
< |
strcpy( cosCorr1, argv[i] ); |
144 |
< |
i++; |
145 |
< |
strcpy( cosCorr2, argv[i] ); |
143 |
> |
flag2Val = strtod( argV[i], &conversionCheck ); |
144 |
> |
if( conversionCheck == argV[i] ) conversionError = 1; |
145 |
> |
if( *conversionCheck != '\0' ) conversionError = 1; |
146 |
> |
|
147 |
> |
if( conversionError ){ |
148 |
> |
|
149 |
> |
fprintf( stderr, |
150 |
> |
"Error converting \"%s\" to a double\n", argV[i] ); |
151 |
> |
usage(); |
152 |
> |
exit(0); |
153 |
> |
} |
154 |
> |
|
155 |
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} |
156 |
|
|
157 |
< |
else if( !strcmp( argv[i], "--MuCorr") ){ |
158 |
< |
calcMuCorr = 1; |
159 |
< |
i++; |
55 |
< |
strcpy( muCorr, argv[i] ); |
157 |
> |
else if( !strcmp( argV[i], "--flag3") ){ |
158 |
> |
flag3 = 1; // set flag3 to be true |
159 |
> |
|
160 |
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} |
161 |
|
|
162 |
< |
else if( !strcmp( argv[i], "--startFrame" ) ){ |
59 |
< |
haveStartFrame = 1; |
60 |
< |
i++; |
61 |
< |
startFrame = atoi(argv[i]); |
62 |
< |
startFrame--; |
63 |
< |
} |
162 |
> |
// anything else is an error |
163 |
|
|
65 |
– |
else if( !strcmp( argv[i], "--endFrame" ) ){ |
66 |
– |
haveEndFrame = 1; |
67 |
– |
i++; |
68 |
– |
endFrame = atoi(argv[i]); |
69 |
– |
} |
70 |
– |
|
164 |
|
else{ |
165 |
|
fprintf( stderr, |
166 |
< |
"Invalid option \"%s\"\n", argv[i] ); |
166 |
> |
"Invalid option \"%s\"\n", argV[i] ); |
167 |
|
usage(); |
168 |
+ |
exit(0); |
169 |
|
} |
170 |
|
} |
171 |
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|
175 |
|
|
176 |
|
done =0; |
177 |
|
j = 1; |
178 |
< |
current_flag = argv[i][j]; |
178 |
> |
currentFlag = argv[i][j]; |
179 |
|
while( (current_flag != '\0') && (!done) ){ |
180 |
|
|
181 |
|
switch(current_flag){ |
182 |
|
|
183 |
+ |
case 'h': |
184 |
+ |
// -h => give the usage help message |
185 |
+ |
|
186 |
+ |
usage(); |
187 |
+ |
exit(0); |
188 |
+ |
break; |
189 |
+ |
|
190 |
|
case 'o': |
191 |
|
// -o <prefix> => the output prefix. |
192 |
|
|
193 |
+ |
j++; |
194 |
+ |
currentFlag = argV[i][j]; |
195 |
+ |
|
196 |
+ |
if( currentFlag != '\0' ) optionError = 1; |
197 |
+ |
|
198 |
+ |
if( optionError ){ |
199 |
+ |
fprintf( stderr, |
200 |
+ |
"\n" |
201 |
+ |
"The -o flag should end an option sequence.\n" |
202 |
+ |
" example: -ro <outname> *NOT* -or <outname>\n" ); |
203 |
+ |
usage(); |
204 |
+ |
exit(0); |
205 |
+ |
} |
206 |
+ |
|
207 |
|
i++; |
208 |
< |
out_prefix = argv[i]; |
209 |
< |
have_prefix = 1; |
208 |
> |
outPrefix = argV[i]; |
209 |
> |
if( outPrefix[0] == '-' ) optionError = 1; |
210 |
> |
|
211 |
> |
if( optionError ){ |
212 |
> |
fprintf( stderr, |
213 |
> |
"\n" |
214 |
> |
"\"%s\" is not a valid out prefix/name.\n" |
215 |
> |
"Out prefix/name should not begin with a dash.\n", |
216 |
> |
outPrefix ); |
217 |
> |
usage(); |
218 |
> |
exit(0); |
219 |
> |
} |
220 |
> |
|
221 |
> |
havePrefix = 1; |
222 |
|
done = 1; |
223 |
|
break; |
224 |
|
|
225 |
< |
case 'h': |
99 |
< |
// -h => give the usage |
100 |
< |
|
101 |
< |
usage(); |
102 |
< |
break; |
225 |
> |
|
226 |
|
|
227 |
|
case 'r': |
228 |
< |
// calculates the rmsd |
228 |
> |
// the r flag |
229 |
|
|
230 |
< |
calcRMSD = 1; |
230 |
> |
rFlag = 1; // set rflag to true |
231 |
|
break; |
232 |
|
|
233 |
< |
case 'g': |
234 |
< |
// calculate all to all g(r) |
233 |
> |
case 'i': |
234 |
> |
// -i <int> set <int> to the iVal |
235 |
|
|
236 |
< |
calcGofR = 1; |
237 |
< |
strcpy( gofR1, "all" ); |
238 |
< |
strcpy( gofR2, "all" ); |
236 |
> |
iFlag = 1; // set iFlag to true |
237 |
> |
j++; |
238 |
> |
currentFlag = argV[i][j]; |
239 |
> |
|
240 |
> |
if( currentFlag != '\0' ) optionError = 1; |
241 |
> |
|
242 |
> |
if( optionError ){ |
243 |
> |
fprintf( stderr, |
244 |
> |
"\n" |
245 |
> |
"The -i flag should end an option sequence.\n" |
246 |
> |
" example: -ri <int> *NOT* -ir <int>\n" ); |
247 |
> |
usage(); |
248 |
> |
exit(0); |
249 |
> |
} |
250 |
> |
|
251 |
> |
i++; |
252 |
> |
iVal = (int)strtol( argV[i], &conversionCheck, 10 ); |
253 |
> |
if( conversionCheck == argV[i] ) conversionError = 1; |
254 |
> |
if( *conversionCheck != '\0' ) conversionError = 1; |
255 |
> |
|
256 |
> |
if( conversionError ){ |
257 |
> |
|
258 |
> |
fprintf( stderr, |
259 |
> |
"Error converting \"%s\" to a int\n", argV[i] ); |
260 |
> |
usage(); |
261 |
> |
exit(0); |
262 |
> |
} |
263 |
> |
|
264 |
> |
done = 1; |
265 |
> |
|
266 |
|
break; |
267 |
|
|
268 |
|
default: |
269 |
|
|
270 |
< |
(void)fprintf(stderr, "Bad option \"-%c\"\n", current_flag); |
270 |
> |
(void)fprintf(stderr, |
271 |
> |
"\n" |
272 |
> |
"Bad option \"-%c\"\n", current_flag); |
273 |
|
usage(); |
274 |
|
} |
275 |
|
j++; |
280 |
|
|
281 |
|
else{ |
282 |
|
|
283 |
< |
if( in_name != NULL ){ |
283 |
> |
|
284 |
> |
// ******************************************************** |
285 |
> |
// for only a single input file, leave this as it is. |
286 |
> |
// ******************************************************** |
287 |
> |
|
288 |
> |
if( inName != NULL ){ |
289 |
|
fprintf( stderr, |
290 |
+ |
"\n" |
291 |
|
"Error at \"%s\", program does not currently support\n" |
292 |
|
"more than one input file.\n" |
293 |
|
"\n", |
294 |
< |
argv[i]); |
294 |
> |
argV[i]); |
295 |
|
usage(); |
296 |
+ |
exit(0); |
297 |
|
} |
298 |
+ |
|
299 |
+ |
inName = argvV[i]; |
300 |
+ |
|
301 |
+ |
// ************************************************************* |
302 |
+ |
|
303 |
+ |
|
304 |
+ |
// ************************************************************ |
305 |
+ |
// To support more than one input file, uncomment the following |
306 |
+ |
// section. |
307 |
+ |
// ************************************************************ |
308 |
|
|
309 |
< |
in_name = argv[i]; |
309 |
> |
|
310 |
> |
nInputs++; |
311 |
> |
currentName = (linkedName *) malloc( sizeof( linkedName ) ); |
312 |
> |
if( currentName == NULL ){ |
313 |
> |
fprintf( stderr, |
314 |
> |
"\n" |
315 |
> |
"Ran out of memory\n" ); |
316 |
> |
exit(0); |
317 |
> |
} |
318 |
> |
|
319 |
> |
strcpy( currentName->name, argV[i] ); |
320 |
> |
|
321 |
> |
currentName->next = headName; |
322 |
> |
headName = currentName; |
323 |
> |
|
324 |
> |
// ********************************************************** |
325 |
> |
// end multiple input files |
326 |
> |
// ********************************************************** |
327 |
|
} |
328 |
|
} |
329 |
|
|
330 |
< |
if(in_name == NULL){ |
330 |
> |
|
331 |
> |
|
332 |
> |
|
333 |
> |
// initialize the input file(s) |
334 |
> |
|
335 |
> |
// *********************************************************** |
336 |
> |
// single file: |
337 |
> |
|
338 |
> |
if(inName == NULL){ |
339 |
> |
|
340 |
> |
fprintf( stderr, |
341 |
> |
"\n" |
342 |
> |
"Error, no input file was given\n"); |
343 |
|
usage(); |
344 |
+ |
exit(0); |
345 |
|
} |
346 |
|
|
347 |
< |
if( !have_prefix ) out_prefix = in_name; |
347 |
> |
inFile = fopen( inName, "r" ); |
348 |
> |
if( inFile == NULL ){ |
349 |
> |
|
350 |
> |
fprintf( stderr, |
351 |
> |
"\n" |
352 |
> |
"Error trying to open \"%s\" for reading\n", |
353 |
> |
inName ); |
354 |
> |
exit(0); |
355 |
> |
} |
356 |
|
|
357 |
+ |
// ************************************************************** |
358 |
+ |
// multiple files: |
359 |
+ |
|
360 |
+ |
if( !nInputs ){ |
361 |
+ |
|
362 |
+ |
fprintf( stderr, |
363 |
+ |
"\n" |
364 |
+ |
"Error, no input files were given\n"); |
365 |
+ |
usage(); |
366 |
+ |
exit(0); |
367 |
+ |
} |
368 |
+ |
|
369 |
+ |
// create the input array |
370 |
+ |
|
371 |
+ |
inputArray = (fileStruct *) calloc( nInputs, sizeof( fileStruct ) ); |
372 |
+ |
if( inputArray == NULL ){ |
373 |
+ |
fprintf(stderr, |
374 |
+ |
"\n" |
375 |
+ |
"Ran out of memory\n" ); |
376 |
+ |
exit(0); |
377 |
+ |
} |
378 |
+ |
|
379 |
+ |
j = nInputs - 1; |
380 |
+ |
currentName = headName; |
381 |
+ |
while( currentName != NULL ){ |
382 |
+ |
|
383 |
+ |
strcopy( inputArray[j].fileName, currentName->name ); |
384 |
+ |
inputArray[i].filePtr = NULL; |
385 |
+ |
j--; |
386 |
+ |
currentName = currentName->next; |
387 |
+ |
} |
388 |
+ |
|
389 |
+ |
// delete linked list |
390 |
+ |
|
391 |
+ |
while( headName != NULL ){ |
392 |
+ |
|
393 |
+ |
currentName = headName; |
394 |
+ |
headName = currentName->next; |
395 |
+ |
|
396 |
+ |
free( currentName ); |
397 |
+ |
} |
398 |
+ |
|
399 |
+ |
|
400 |
+ |
// open the files for reading |
401 |
+ |
|
402 |
+ |
for(i=0; i<nInputs; i++){ |
403 |
+ |
|
404 |
+ |
inputArray[i].filePtr = fopen( inName, "r" ); |
405 |
+ |
if( inputArray[i].filePtr == NULL ){ |
406 |
+ |
|
407 |
+ |
fprintf( stderr, |
408 |
+ |
"\n" |
409 |
+ |
"Error trying to open \"%s\" for reading\n", |
410 |
+ |
inputArray[i].fileName ); |
411 |
+ |
exit(0); |
412 |
+ |
} |
413 |
+ |
|
414 |
+ |
//read and do stuff here |
415 |
+ |
|
416 |
+ |
} |
417 |
+ |
|
418 |
+ |
// ************************************************************* |
419 |
+ |
// end file opening |
420 |
+ |
// ************************************************************* |
421 |
+ |
|
422 |
+ |
|
423 |
+ |
|
424 |
+ |
// or read files here |
425 |
+ |
|
426 |
+ |
|
427 |
+ |
|
428 |
+ |
|
429 |
+ |
|
430 |
+ |
// close files when we are done. |
431 |
+ |
|
432 |
+ |
// *********************************************************** |
433 |
+ |
// single: |
434 |
+ |
|
435 |
+ |
fclose( inFile ); |
436 |
+ |
|
437 |
+ |
// ************************************************************* |
438 |
+ |
// multiple: |
439 |
+ |
|
440 |
+ |
for( i=0; i<nInputs; i++){ |
441 |
+ |
|
442 |
+ |
fclose( inputArray[i].filePtr ); |
443 |
+ |
} |
444 |
+ |
|
445 |
+ |
free( inputArray ); // free the input Array if we are done; |
446 |
+ |
inputArray = NULL; |
447 |
+ |
|
448 |
+ |
// ************************************************************ |
449 |
+ |
// end file closing |
450 |
+ |
// ************************************************************ |
451 |
+ |
|
452 |
|
} |
453 |
|
|
454 |
|
|
467 |
|
" -h Display this message\n" |
468 |
|
" -o <name> The output name/prefix\n" |
469 |
|
" -r the r flag\n" |
470 |
< |
" -i <#> set number to <#>\n" |
470 |
> |
" -i <int> set number to <#>\n" |
471 |
|
|
472 |
|
"\n" |
473 |
|
" long:\n" |
474 |
|
" -----\n" |
475 |
|
" --flag1 <arg1> <arg2> does flag 1 for arg1 and 2\n" |
476 |
< |
" --flag2 <arg1> does flag 2 for arg1\n" |
476 |
> |
" --flag2 <double> does flag 2 for double\n" |
477 |
|
" --flag3 does flag 3\n" |
478 |
|
|
479 |
|
"\n" |
480 |
|
"\n", |
481 |
< |
program_name); |
482 |
< |
exit(8); |
481 |
> |
program_name) |
482 |
> |
exit(0); |
483 |
|
} |