helpString += "The phylip parameter allows you to enter your distance file.";
helpString += "The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True";
helpString += "Example pcoa(phylip=yourDistanceFile).\n";
- helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n";
return helpString;
}
catch(exception& e) {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
phylipfile = m->getPhylipFile();
if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setPhylipFile(phylipfile); }
filename = phylipfile;
vector<vector<double> > G = D;
//vector<vector<double> > copy_G;
- m->mothurOut("\nProcessing...\n\n");
+ m->mothurOut("\nProcessing...\n");
for(int count=0;count<2;count++){
linearCalc.recenter(offset, D, G); if (m->control_pressed) { return 0; }
output(fbase, names, G, d);
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (metric) {
vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}
}