//**********************************************************************************************************************
vector<string> MGClusterCommand::setParameters(){
try {
CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "average", "", "", "",false,false); parameters.push_back(pmethod);
CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
CommandParameter pmin("min", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmin);
CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmerge);
CommandParameter phcluster("hcluster", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phcluster);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "MGClusterCommand", "setParameters");
exit(1);
}
}
void copy(char *fromDir, char *fname, char *toDir)
{
FILE *nul; /* nul will redirect stdout to DOS 'nul' */
char from[FILENAME_MAX], to[FILENAME_MAX], comd[128];
int bytesRead, oldStdout;
/* Create the strings to describe the paths */
pmerge(from, NULL, fromDir, fname, NULL);
pmerge(to, NULL, toDir, fname, NULL);
/* Construct 'comd' string which is a dos command for a copy */
strcpy(comd, "copy ");
strcat(comd, from); strcat(comd, " ");
strcat(comd, to);
/* Redirect stdout to a nul file, kills output to the screen */
nul = fopen("NUL", "w");
oldStdout = dup(STDOUT);
dup2(fileno(nul), STDOUT);
fclose(nul);
system(comd); /* COPY file */
/* Restore stdout and close nul file */
dup2(oldStdout, STDOUT);
close(oldStdout);
/* Display file source and target, */
/* otherwise comment out the next line. */
printf("\n%s copied to %s",from,to);
}
