int MatrixOutputCommand::execute(){
try {
int count = 1;
- EstOutput data;
- vector<SharedRAbundVector*> subset;
-
+
//if the users entered no valid calculators don't execute command
if (matrixCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; }
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
+ vector<SharedRAbundVector*> lastLookup = lookup;
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = globaldata->labels;
if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0;}
numGroups = globaldata->Groups.size();
- while(lookup[0] != NULL){
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
-
cout << lookup[0]->getLabel() << '\t' << count << endl;
+ process(lookup);
- //for each calculator
- for(int i = 0 ; i < matrixCalculators.size(); i++) {
-
- //initialize simMatrix
- simMatrix.clear();
- simMatrix.resize(numGroups);
- for (int m = 0; m < simMatrix.size(); m++) {
- for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[m].push_back(0.0);
- }
- }
-
- for (int k = 0; k < lookup.size(); k++) {
- for (int l = k; l < lookup.size(); l++) {
- if (k != l) { //we dont need to similiarity of a groups to itself
- //get estimated similarity between 2 groups
-
- subset.clear(); //clear out old pair of sharedrabunds
- //add new pair of sharedrabunds
- subset.push_back(lookup[k]); subset.push_back(lookup[l]);
-
- data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
- //save values in similarity matrix
- simMatrix[k][l] = 1.0 - data[0]; //convert similiarity to distance
- simMatrix[l][k] = 1.0 - data[0]; //convert similiarity to distance
- }
- }
- }
-
- exportFileName = getRootName(globaldata->inputFileName) + matrixCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".dist";
- openOutputFile(exportFileName, out);
- printSims(out);
- out.close();
-
- }
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
}
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ process(lastLookup);
+
+ processedLabels.insert(lastLookup[0]->getLabel());
+ userLabels.erase(lastLookup[0]->getLabel());
+ }
+
//prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
+ lastLookup = lookup;
//get next line to process
lookup = input->getSharedRAbundVectors();
count++;
}
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
+ cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ process(lastLookup);
+ }
+
+ for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
+
+
//reset groups parameter
globaldata->Groups.clear(); globaldata->setGroups("");
}
}
/***********************************************************/
+void MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
+ try {
+
+ EstOutput data;
+ vector<SharedRAbundVector*> subset;
+
+ //for each calculator
+ for(int i = 0 ; i < matrixCalculators.size(); i++) {
+
+ //initialize simMatrix
+ simMatrix.clear();
+ simMatrix.resize(numGroups);
+ for (int m = 0; m < simMatrix.size(); m++) {
+ for (int j = 0; j < simMatrix.size(); j++) {
+ simMatrix[m].push_back(0.0);
+ }
+ }
+
+ for (int k = 0; k < thisLookup.size(); k++) {
+ for (int l = k; l < thisLookup.size(); l++) {
+ if (k != l) { //we dont need to similiarity of a groups to itself
+ //get estimated similarity between 2 groups
+
+ subset.clear(); //clear out old pair of sharedrabunds
+ //add new pair of sharedrabunds
+ subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
+
+ data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
+ //save values in similarity matrix
+ simMatrix[k][l] = 1.0 - data[0]; //convert similiarity to distance
+ simMatrix[l][k] = 1.0 - data[0]; //convert similiarity to distance
+ }
+ }
+ }
+
+ exportFileName = getRootName(globaldata->inputFileName) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
+ openOutputFile(exportFileName, out);
+ printSims(out);
+ out.close();
+
+ }
+
+
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the MatrixOutputCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+
projects / mothur.git / blobdiff