//**********************************************************************************************************************
vector<string> MatrixOutputCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "",false,false); parameters.push_back(pmode);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","phylip",false,true,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "","",false,false); parameters.push_back(pmode);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ 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); }
}
}
//**********************************************************************************************************************
-string MatrixOutputCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MatrixOutputCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "phylip") { outputFileName = "dist"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "MatrixOutputCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "phylip") { pattern = "[filename],[calc],[distance],[outputtag],dist-[filename],[calc],[distance],[outputtag],[tag2],dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
MatrixOutputCommand::MatrixOutputCommand(){
else { subsample = false; }
}
- if (subsample == false) { iters = 1; }
+ if (subsample == false) { iters = 0; }
if (abort == false) {
try {
vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.size());
-
+
for (int thisIter = 0; thisIter < iters+1; thisIter++) {
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[tag2]"] = "";
vector<SharedRAbundVector*> thisItersLookup = thisLookup;
matrix[column][row] = dist;
}
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + "." + getOutputFileNameTag("phylip");
+ variables["[outputtag]"] = output;
+ variables["[calc]"] = matrixCalculators[i]->getName();
+ string distFileName = getOutputFileName("phylip",variables);
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
+
ofstream outDist;
m->openOutputFile(distFileName, outDist);
outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
}
- if (iters != 1) {
+ if (iters != 0) {
//we need to find the average distance and standard deviation for each groups distance
vector< vector<seqDist> > calcAverages; calcAverages.resize(matrixCalculators.size());
stdmatrix[row][column] = stdDist;
stdmatrix[column][row] = stdDist;
}
-
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".ave." + getOutputFileNameTag("phylip");
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[outputtag]"] = output;
+ variables["[tag2]"] = "ave";
+ variables["[calc]"] = matrixCalculators[i]->getName();
+ string distFileName = getOutputFileName("phylip",variables);
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
ofstream outAve;
m->openOutputFile(distFileName, outAve);
outAve.close();
- distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".std." + getOutputFileNameTag("phylip");
+ variables["[tag2]"] = "std";
+ distFileName = outputDir + getOutputFileName("phylip",variables);
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
ofstream outSTD;
m->openOutputFile(distFileName, outSTD);