forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index b3d359ca53aa31fa10fe209cf0cd52946c2fd79b..652ff4e49ecf163fc71dad48b40eb1485012b105 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -282,9 +282,15 @@ int RareFactCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
+        map<string, set<int> > labelToEnds;
                if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
-               else {  inputFileNames = parseSharedFile(sharedfile);  format = "rabund"; }
-                               
+               else {  inputFileNames = parseSharedFile(sharedfile, labelToEnds);  format = "rabund"; }
+               for (map<string, set<int> >::iterator it = labelToEnds.begin(); it != labelToEnds.end(); it++) {
+            cout << it->first << endl;
+            for (set<int>::iterator its = (it->second).begin(); its != (it->second).end(); its++) {
+                cout << (*its) << endl;
+            }
+        }
                if (m->control_pressed) { return 0; }
                
                map<int, string> file2Group; //index in outputNames[i] -> group
@@ -378,7 +384,10 @@ int RareFactCommand::execute(){
                                if(allLines == 1 || labels.count(order->getLabel()) == 1){
                                        
                                        m->mothurOut(order->getLabel()); m->mothurOutEndLine();
-                                       rCurve = new Rarefact(order, rDisplays, processors);
+                    map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
+                    set<int> ends;
+                    if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
+                                       rCurve = new Rarefact(order, rDisplays, processors, ends);
                                        rCurve->getCurve(freq, nIters);
                                        delete rCurve;
                                        
@@ -393,7 +402,11 @@ int RareFactCommand::execute(){
                                        order = (input->getOrderVector(lastLabel));
                                        
                                        m->mothurOut(order->getLabel()); m->mothurOutEndLine();
-                                       rCurve = new Rarefact(order, rDisplays, processors);
+                                       map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
+                    set<int> ends;
+                    if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
+                                       rCurve = new Rarefact(order, rDisplays, processors, ends);
+
                                        rCurve->getCurve(freq, nIters);
                                        delete rCurve;
                                        
@@ -433,7 +446,11 @@ int RareFactCommand::execute(){
                                order = (input->getOrderVector(lastLabel));
                                
                                m->mothurOut(order->getLabel()); m->mothurOutEndLine();
-                               rCurve = new Rarefact(order, rDisplays, processors);
+                               map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
+                set<int> ends;
+                if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
+                rCurve = new Rarefact(order, rDisplays, processors, ends);
+
                                rCurve->getCurve(freq, nIters);
                                delete rCurve;
                                
@@ -625,7 +642,7 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
        }
 }
 //**********************************************************************************************************************
-vector<string> RareFactCommand::parseSharedFile(string filename) {
+vector<string> RareFactCommand::parseSharedFile(string filename, map<string, set<int> >& label2Ends) {
        try {
                vector<string> filenames;
                
@@ -657,6 +674,7 @@ vector<string> RareFactCommand::parseSharedFile(string filename) {
                                m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
                                rav.print(*(filehandles[lookup[i]->getGroup()]));
                                (*(filehandles[lookup[i]->getGroup()])).close();
+                label2Ends[lookup[i]->getLabel()].insert(rav.getNumSeqs());
                        }
                
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }