input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
+ lastLookup = lookup;
if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0; }
void TreeGroupCommand::makeSimsShared() {
try {
int count = 1;
- EstOutput data;
- vector<SharedRAbundVector*> subset;
- numGroups = globaldata->Groups.size();
-
//clear globaldatas old tree names if any
globaldata->Treenames.clear();
tmap->makeSim(globaldata->gGroupmap);
globaldata->gTreemap = tmap;
- while(lookup[0] != NULL){
+ set<string> processedLabels;
+ set<string> userLabels = globaldata->labels;
+
+ //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);
+
+ 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
+ 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]; }
+ for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************/
+void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
+ try{
+ EstOutput data;
+ vector<SharedRAbundVector*> subset;
+ numGroups = globaldata->Groups.size();
//for each calculator
for(int i = 0 ; i < treeCalculators.size(); i++) {
for (int g = 0; g < numGroups; g++) { index[g] = g; }
//create a new filename
- outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".tre";
+ outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
- for (int k = 0; k < lookup.size(); k++) {
- for (int l = k; l < lookup.size(); l++) {
+ 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(lookup[k]); subset.push_back(lookup[l]);
+ subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
//save values in similarity matrix
//creates tree from similarity matrix and write out file
createTree();
}
- }
-
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
-
- //get next line to process
- lookup = input->getSharedRAbundVectors();
- count++;
- }
-
- for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the TreeGroupCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
-
/***********************************************************/
+
projects / mothur.git / blobdiff