void writeMessagePointer(const MessageSeverity* messServer){
writeElapsedTime();
messServer->writeMessage();
}
int main(int argc, char **argv) {
char *shortSequence = NULL,
*longSequence = NULL, /* eventually point to buffers for the two sequences */
*outputPath = NULL; /* eventually points to the path for the output */
int shortLength=0, longLength=0; /* space required for each of those buffers */
int repetitions = 1; /* number of repetitions: one is the default */
int n; /* index into argv array */
long start, iterationStart, dataRead, scoringDone; /* timestamps to compute elapsed time */
const char * const usage = "sw: usage is \r\n\tsw -s shortPath -l longPath -p paramPath [-o outputPath] [-r repetitions]\r\n.\r\n";
const char * const phases[] = {"Input phase:", "Scoring phase:", "Traceback phase:"};
int rc = 0;
buffer = malloc(BUFFER_SIZE*sizeof(char));
Output output;
output.shorterPath = output.longerPath = NULL;
for(n=1; n<argc-1; n+=2) { /* pull the sequence number from the command line */
char *value = argv[n+1];
switch(argv[n][1]) {
case 's': output.shorterPath = value; break;
case 'l': output.longerPath = value; break;
case 'o': outputPath = value; break;
case 'p': readParameters(value); break;
case 'r': repetitions = atoi(value); break;
default:
fprintf(stderr, usage);
return 10;
}
}
if (alphabetSize == 0) { /* no point in proceeding if parameters are not correct */
fprintf(stderr, "No parameter path supplied or parameters are incorrect\n%s", usage);
rc = 19;
}
if (output.shorterPath == NULL) {
fprintf(stderr, "No path for shorter sequence supplied\n%s", usage);
rc = 20;
}
if (output.longerPath == NULL) {
fprintf(stderr, "No path for longer sequence supplied\n%s", usage);
rc = 21;
}
free(buffer);
if (rc > 0) return rc;
start = nowInMilliseconds();
startTimings(&output, repetitions, 3, phases);
for(n = 0; n<repetitions; n++) {
output.phases = 0;
output.iterations = n;
iterationStart = nowInMilliseconds();
shortSequence = readASequence(output.shorterPath);
shortLength = 1+strlen(shortSequence); /* this is the WHOLE BUFFER SIZE: add 1 for the sentinel 0 byte */
longSequence = readASequence(output.longerPath);
longLength = 1+strlen(longSequence); /* this is the WHOLE BUFFER SIZE: add 1 for the sentinel 0 byte */
dataRead = writeElapsedTime(&output, iterationStart);
computeTheBestScores(shortSequence, shortLength, longSequence, longLength);
scoringDone = writeElapsedTime(&output, dataRead);
doTheTraceback(shortSequence, shortLength, longSequence, longLength, &output);
writeElapsedTime(&output, scoringDone);
free(shortSequence);
free(longSequence);
}
writeOutput(&output, outputPath, (int)(nowInMilliseconds()-start));
return 0;
}
void writeMessageReference(const MessageSeverity& messServer){
writeElapsedTime();
messServer.writeMessage();
}
