fixing minor bugs

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 22dc2e9f7ab15a671f4a3dd699ca570655b688a4..dd900643a741d576d1595c1a9c346d6b6c334361 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -36,15 +36,19 @@ SharedCommand::SharedCommand(){
 int SharedCommand::execute(){
        try {
                globaldata = GlobalData::getInstance();
+               //lookup.clear();
                int count = 1;
                string errorOff = "no error";
                        
                //read in listfile
                read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
+
                input = globaldata->ginput;
                SharedList = globaldata->gSharedList;
                SharedListVector* lastList = SharedList;
+               //lookup = SharedList->getSharedRAbundVector();
+               //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;
@@ -55,9 +59,9 @@ int SharedCommand::execute(){
                
                while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
                        
-                                               
+
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
-                       
+                                       
                                        shared->getSharedVectors(SharedList); //fills sharedGroups with new info and updates sharedVector
                                        printSharedData(); //prints info to the .shared file
                                
@@ -76,8 +80,11 @@ int SharedCommand::execute(){
                        
                        if (count != 1) { delete lastList; }
                        lastList = SharedList;                  
-
                        SharedList = input->getSharedListVector(); //get new list vector to process
+                       
+                       //if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
+                       //lastLookup = lookup; 
+                       //if (SharedList != NULL) { lookup = SharedList->getSharedRAbundVector(); }
                }
                
                //output error messages about any remaining user labels
@@ -101,6 +108,7 @@ int SharedCommand::execute(){
                
                delete lastList;
                delete shared;
+               out.close();
                
                return 0;
        }
@@ -117,6 +125,12 @@ int SharedCommand::execute(){
 //**********************************************************************************************************************
 void SharedCommand::printSharedData() {
        try {
+       
+               ///for (int i = 0; i < thislookup.size(); i++) {
+               //      out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+//cout << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl;                      
+               //      thislookup[i]->print(out);
+       //      }
                //prints out horizontally
                for (it = shared->sharedGroups.begin(); it != shared->sharedGroups.end(); it++) {
                        out << it->second->getLabel() << "\t" << it->first << "\t"; //prints out label and groupname