- globaldata = GlobalData::getInstance();
- convert(globaldata->getCutOff(), cutOff);
- convert(globaldata->getIters(), iters);
- convert(globaldata->getStep(), step);
- form = globaldata->getForm();
- matrix = globaldata->gMatrix;
- coverageFile = getRootName(globaldata->getPhylipFile()) + "coverage";
- summaryFile = getRootName(globaldata->getPhylipFile()) + "slsummary";
- openOutputFile(coverageFile, out);
- openOutputFile(summaryFile, outSum);
-
- //set the groups to be analyzed
- setGroups();
-
- //file headers for coverage file
- out << "D" << '\t';
- for (int i = 0; i < groupComb.size(); i++) {
- out << "C" + groupComb[i] << '\t';
- }
-
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- //don't output AA to AA
- if (i != j) {
- out << "Delta" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
- }
- }
- }
- out << endl;
-
- numComp = numGroups*numGroups;
-
- coverage = new Coverage();
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","coverage-libshuffsummary",false,true,true); parameters.push_back(pphylip);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter piters("iters", "Number", "", "10000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pstep("step", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(pstep);
+ CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pform("form", "Multiple", "discrete-integral", "integral", "", "", "","",false,false); parameters.push_back(pform);
+ CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);