//**********************************************************************************************************************
vector<string> OtuHierarchyCommand::setParameters(){
try {
- CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otuheirarchy",false,true,true); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ 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 OtuHierarchyCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "otuheirarchy") { pattern = "[filename],[distance1],[tag],[distance2],otu.hierarchy"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
OtuHierarchyCommand::OtuHierarchyCommand(){
try {
abort = true;
}
}else if (listFile == "not open") { abort = true; }
+ else { m->setListFile(listFile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
}
//map sequences to bin number in the "little" otu
- map<string, int> littleBins;
+ map<string, int> littleBins;
+ vector<string> binLabels0 = lists[0].getLabels();
for (int i = 0; i < lists[0].getNumBins(); i++) {
if (m->control_pressed) { return 0; }
-
- string names = lists[0].get(i);
-
- //parse bin
- while (names.find_first_of(',') != -1) {
- string name = names.substr(0,names.find_first_of(','));
- names = names.substr(names.find_first_of(',')+1, names.length());
- littleBins[name] = i;
- }
-
- //get last name
- littleBins[names] = i;
- }
+ string bin = lists[0].get(i);
+ vector<string> names; m->splitAtComma(bin, names);
+ for (int j = 0; j < names.size(); j++) { littleBins[names[j]] = i; }
+ }
ofstream out;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
+ variables["[distance1]"] = lists[0].getLabel();
+ variables["[tag]"] = "-";
+ variables["[distance2]"] = lists[1].getLabel();
+ string outputFileName = getOutputFileName("otuheirarchy",variables);
m->openOutputFile(outputFileName, out);
//go through each bin in "big" otu and output the bins in "little" otu which created it
+ vector<string> binLabels1 = lists[1].getLabels();
for (int i = 0; i < lists[1].getNumBins(); i++) {
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
- string names = lists[1].get(i);
+ string binnames = lists[1].get(i);
+ vector<string> names; m->splitAtComma(binnames, names);
//output column 1
- if (output == "name") { out << names << '\t'; }
- else { out << i << '\t'; }
+ if (output == "name") { out << binnames << '\t'; }
+ else { out << binLabels1[i] << '\t'; }
map<int, int> bins; //bin numbers in little that are in this bin in big
map<int, int>::iterator it;
//parse bin
- while (names.find_first_of(',') != -1) {
- string name = names.substr(0,names.find_first_of(','));
- names = names.substr(names.find_first_of(',')+1, names.length());
- bins[littleBins[name]] = littleBins[name];
- }
-
- //get last name
- bins[littleBins[names]] = littleBins[names];
+ for (int j = 0; j < names.size(); j++) { bins[littleBins[names[j]]] = littleBins[names[j]]; }
string col2 = "";
for (it = bins.begin(); it != bins.end(); it++) {
if (output == "name") { col2 += lists[0].get(it->first) + "\t"; }
- else { col2 += toString(it->first) + "\t"; }
+ else { col2 += binLabels0[it->first] + "\t"; }
}
//output column 2
out.close();
- if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName);
m->mothurOutEndLine();