setParameters();
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
- outputTypes["subsample"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
- outputTypes["subsample"] = 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);
set<string> userLabels = labels;
if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0;}
-
- numGroups = lookup.size();
- lines.resize(processors);
- for (int i = 0; i < processors; i++) {
- lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
- lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
- }
if (subsample) {
if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
lookup = temp;
m->setGroups(Groups);
}
+
+ if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return 0; }
}
-
+
+ numGroups = lookup.size();
+ lines.resize(processors);
+ for (int i = 0; i < processors; i++) {
+ lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
+ lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
+ }
+
if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
//as long as you are not at the end of the file or done wih the lines you want
out << simMatrix.size() << endl;
if (output == "lt") {
- for (int m = 0; m < simMatrix.size(); m++) {
- out << lookup[m]->getGroup() << '\t';
- for (int n = 0; n < m; n++) {
- out << simMatrix[m][n] << '\t';
+ for (int b = 0; b < simMatrix.size(); b++) {
+ out << lookup[b]->getGroup() << '\t';
+ for (int n = 0; n < b; n++) {
+ out << simMatrix[b][n] << '\t';
}
out << endl;
}
}else{
- for (int m = 0; m < simMatrix.size(); m++) {
- out << lookup[m]->getGroup() << '\t';
- for (int n = 0; n < simMatrix[m].size(); n++) {
- out << simMatrix[m][n] << '\t';
+ for (int b = 0; b < simMatrix.size(); m++) {
+ out << lookup[b]->getGroup() << '\t';
+ for (int n = 0; n < simMatrix[b].size(); n++) {
+ out << simMatrix[b][n] << '\t';
}
out << endl;
}
/***********************************************************/
int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
try {
- EstOutput data;
- vector<SharedRAbundVector*> subset;
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; thisIter++) {
+ for (int thisIter = 0; thisIter < iters+1; thisIter++) {
vector<SharedRAbundVector*> thisItersLookup = thisLookup;
- if (subsample) {
+ if (subsample && (thisIter != 0)) {
SubSample sample;
vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
#endif
}
- calcDistsTotals.push_back(calcDists);
-
- if (subsample) {
-
+ if (subsample && (thisIter != 0)) {
+ calcDistsTotals.push_back(calcDists);
//clean up memory
for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
thisItersLookup.clear();
for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
+ }else { //print results for whole dataset
+ for (int i = 0; i < calcDists.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ //initialize matrix
+ vector< vector<double> > matrix; //square matrix to represent the distance
+ matrix.resize(thisLookup.size());
+ for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
+
+ for (int j = 0; j < calcDists[i].size(); j++) {
+ int row = calcDists[i][j].seq1;
+ int column = calcDists[i][j].seq2;
+ double dist = calcDists[i][j].dist;
+
+ matrix[row][column] = dist;
+ matrix[column][row] = dist;
+ }
+
+ string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
+ 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);
+
+ printSims(outDist, matrix);
+
+ outDist.close();
+ }
}
}
outSTD.close();
}
- }else {
-
- for (int i = 0; i < calcDists.size(); i++) {
- if (m->control_pressed) { break; }
-
- //initialize matrix
- vector< vector<double> > matrix; //square matrix to represent the distance
- matrix.resize(thisLookup.size());
- for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
-
- for (int j = 0; j < calcDists[i].size(); j++) {
- int row = calcDists[i][j].seq1;
- int column = calcDists[i][j].seq2;
- double dist = calcDists[i][j].dist;
-
- matrix[row][column] = dist;
- matrix[column][row] = dist;
- }
-
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
- 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);
-
- printSims(outDist, matrix);
-
- outDist.close();
- }
}
return 0;
projects / mothur.git / blobdiff