//********************************************************************************************************************** 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); }