added hcluster command and fixed some bugs, namely one with smart distancing.

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 62d8b3a3cf3f07a42a1d1f77c3ce21d57d526cdb..727a04b273fc3ee4b4c9c5882f55e746ad2c0d6a 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -52,6 +52,7 @@ int SharedCommand::execute(){
                
                //lookup.clear();
                string errorOff = "no error";
+               //errorOff = "";
                        
                //read in listfile
                read = new ReadOTUFile(globaldata->inputFileName);      
@@ -83,8 +84,7 @@ int SharedCommand::execute(){
                
                //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<string> userLabels = globaldata->labels;    
                
                while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
                        
@@ -102,6 +102,8 @@ int SharedCommand::execute(){
                        }
                        
                        if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+                                       string saveLabel = SharedList->getLabel();
+                                       
                                        delete SharedList;
                                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
                                        
@@ -113,6 +115,9 @@ int SharedCommand::execute(){
                                        
                                        processedLabels.insert(SharedList->getLabel());
                                        userLabels.erase(SharedList->getLabel());
+                                       
+                                       //restore real lastlabel to save below
+                                       SharedList->setLabel(saveLabel);
                        }
                        
                
@@ -166,6 +171,7 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
                
                //initialize bin values
                for (int i = 0; i < thislookup.size(); i++) {
+//cout << "in printData " << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() <<  endl;
                        out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
                        thislookup[i]->print(out);