//**********************************************************************************************************************
vector<string> CorrAxesCommand::setParameters(){
try {
- CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paxes);
- CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata);
- CommandParameter pnumaxes("numaxes", "Number", "", "3", "", "", "",false,false); parameters.push_back(pnumaxes);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none","corraxes",false,true,true); parameters.push_back(paxes);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false,true); parameters.push_back(prelabund);
+ CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false); parameters.push_back(pmetadata);
+ CommandParameter pnumaxes("numaxes", "Number", "", "3", "", "", "","",false,false); parameters.push_back(pnumaxes);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false); parameters.push_back(pmethod);
+ 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); }
exit(1);
}
}
+//**********************************************************************************************************************
+string CorrAxesCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "corraxes") { pattern = "[filename],[tag],corr.axes"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
CorrAxesCommand::CorrAxesCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["corr.axes"] = tempOutNames;
+ outputTypes["corraxes"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "CorrAxesCommand", "CorrAxesCommand");
}
vector<string> tempOutNames;
- outputTypes["corr.axes"] = tempOutNames;
+ outputTypes["corraxes"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
/*************************************************************************************/
// calc the r values //
/************************************************************************************/
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + ".corr.axes";
- outputNames.push_back(outputFileName); outputTypes["corr.axes"].push_back(outputFileName);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ variables["[tag]"] = method;
+ string outputFileName = getOutputFileName("corraxes", variables);
+ outputNames.push_back(outputFileName); outputTypes["corraxes"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
m->openInputFile(metadatafile, in);
string headerLine = m->getline(in); m->gobble(in);
- istringstream iss (headerLine,istringstream::in);
-
- //read the first label, because it refers to the groups
- string columnLabel;
- iss >> columnLabel; m->gobble(iss);
+ vector<string> pieces = m->splitWhiteSpace(headerLine);
//save names of columns you are reading
- while (!iss.eof()) {
- iss >> columnLabel; m->gobble(iss);
- metadataLabels.push_back(columnLabel);
+ for (int i = 1; i < pieces.size(); i++) {
+ metadataLabels.push_back(pieces[i]);
}
int count = metadataLabels.size();