int BootSharedCommand::execute(){
try {
int count = 1;
- EstOutput data;
- vector<SharedRAbundVector*> subset;
//if the users entered no valid calculators don't execute command
if (treeCalculators.size() == 0) { return 0; }
read->read(&*globaldata);
input = globaldata->ginput;
order = input->getSharedOrderVector();
+ SharedOrderVector* lastOrder = order;
+
+ //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;
//set users groups
util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
tmap->makeSim(globaldata->gGroupmap);
globaldata->gTreemap = tmap;
- while(order != NULL){
+ while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
cout << order->getLabel() << '\t' << count << endl;
+ process(order);
- //open an ostream for each calc to print to
- for (int z = 0; z < treeCalculators.size(); z++) {
- //create a new filename
- outputFile = getRootName(globaldata->inputFileName) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
- openOutputFile(outputFile, *(out[z]));
- }
-
- //create a file for each calculator with the 1000 trees in it.
- for (int p = 0; p < iters; p++) {
-
- util->getSharedVectorswithReplacement(globaldata->Groups, lookup, order); //fills group vectors from order vector.
-
- //for each calculator
- for(int i = 0 ; i < treeCalculators.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);
- }
- }
-
- //initialize index
- index.clear();
- for (int g = 0; g < numGroups; g++) { index[g] = g; }
-
- for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare
- for (int l = k; l < lookup.size(); l++) {
- if (k != l) { //we dont need to similiarity of a groups to itself
- subset.clear(); //clear out old pair of sharedrabunds
- //add new pair of sharedrabunds
- subset.push_back(lookup[k]); subset.push_back(lookup[l]);
-
- //get estimated similarity between 2 groups
- data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
- //save values in similarity matrix
- simMatrix[k][l] = data[0];
- simMatrix[l][k] = data[0];
- }
- }
- }
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
- //creates tree from similarity matrix and write out file
- createTree(out[i]);
- }
- }
- //close ostream for each calc
- for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
+ //you have a label the user want that is smaller than this line and the last line has not already been processed
}
-
+
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
+
+ cout << lastOrder->getLabel() << '\t' << count << endl;
+ process(lastOrder);
+
+ processedLabels.insert(lastOrder->getLabel());
+ userLabels.erase(lastOrder->getLabel());
+ }
+
+ if (count != 1) { delete lastOrder; }
+ lastOrder = order;
+
//get next line to process
order = input->getSharedOrderVector();
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(lastOrder->getLabel()) != 1) {
+ cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ process(lastOrder);
+ cout << lastOrder->getLabel() << '\t' << count << endl;
+ }
+
+ delete lastOrder;
+
//reset groups parameter
globaldata->Groups.clear(); globaldata->setGroups("");
}
}
/***********************************************************/
+void BootSharedCommand::process(SharedOrderVector* order) {
+ try{
+ EstOutput data;
+ vector<SharedRAbundVector*> subset;
+
+ //open an ostream for each calc to print to
+ for (int z = 0; z < treeCalculators.size(); z++) {
+ //create a new filename
+ outputFile = getRootName(globaldata->inputFileName) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
+ openOutputFile(outputFile, *(out[z]));
+ }
+
+ //create a file for each calculator with the 1000 trees in it.
+ for (int p = 0; p < iters; p++) {
+
+ util->getSharedVectorswithReplacement(globaldata->Groups, lookup, order); //fills group vectors from order vector.
+
+ //for each calculator
+ for(int i = 0 ; i < treeCalculators.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);
+ }
+ }
+
+ //initialize index
+ index.clear();
+ for (int g = 0; g < numGroups; g++) { index[g] = g; }
+
+ for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare
+ for (int l = k; l < lookup.size(); l++) {
+ if (k != l) { //we dont need to similiarity of a groups to itself
+ subset.clear(); //clear out old pair of sharedrabunds
+ //add new pair of sharedrabunds
+ subset.push_back(lookup[k]); subset.push_back(lookup[l]);
+
+ //get estimated similarity between 2 groups
+ data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
+ //save values in similarity matrix
+ simMatrix[k][l] = data[0];
+ simMatrix[l][k] = data[0];
+ }
+ }
+ }
+
+ //creates tree from similarity matrix and write out file
+ createTree(out[i]);
+ }
+ }
+ //close ostream for each calc
+ for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BootSharedCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+
projects / mothur.git / blobdiff