changed raredisplay to use vectors instead of files

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 6ca1ed63585463d92ac8dc7aa65f921ca1070308..c49e56ac8d9264f535a7b9c6f7457948f421f69a 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -20,23 +20,36 @@ SharedCommand::SharedCommand(){
                filename = getRootName(filename);
                filename = filename + "shared";
                openOutputFile(filename, out);
+               
+               groupMap = globaldata->gGroupmap;
+               
+               //fill filehandles with neccessary ofstreams
+               int i;
+               ofstream* temp;
+               for (i=0; i<groupMap->getNumGroups(); i++) {
+                       temp = new ofstream;
+                       filehandles[groupMap->namesOfGroups[i]] = temp;
+               }
+               
+               //set fileroot
+               fileroot = getRootName(globaldata->getListFile());
+               
+               //clears file before we start to write to it below
+               for (int i=0; i<groupMap->getNumGroups(); i++) {
+                       remove((fileroot + groupMap->namesOfGroups[i] + ".rabund").c_str());
+               }
+
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedCommand class function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedCommand", "SharedCommand");
                exit(1);
        }
-
 }
 //**********************************************************************************************************************
 
 int SharedCommand::execute(){
        try {
                
-               cout << "creating sharedfile...";
                //lookup.clear();
                int count = 1;
                string errorOff = "no error";
@@ -60,7 +73,10 @@ int SharedCommand::execute(){
                        
 
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+                                       
                                        lookup = SharedList->getSharedRAbundVector();
+                                       mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+                                       
                                        printSharedData(lookup); //prints info to the .shared file
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                                
@@ -74,6 +90,8 @@ int SharedCommand::execute(){
                                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
                                        
                                        lookup = SharedList->getSharedRAbundVector();
+                                       mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+                                       
                                        printSharedData(lookup); //prints info to the .shared file
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                                        
@@ -94,12 +112,8 @@ int SharedCommand::execute(){
                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(lastLabel) != 1) {
-                               //cout << ". I will use " << lastList->getLabel() << "." << endl;
                                needToRun = true;
-                       }else {
-                               //cout << ". Please refer to " << lastList->getLabel() << "." << endl;
                        }
                }
                
@@ -109,6 +123,8 @@ int SharedCommand::execute(){
                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
                                        
                        lookup = SharedList->getSharedRAbundVector();
+                       mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+                       
                        printSharedData(lookup); //prints info to the .shared file
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                        delete SharedList;
@@ -119,18 +135,17 @@ int SharedCommand::execute(){
                
                out.close();
                
-               cout << "complete." << endl;
+               for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+                       delete it3->second;
+               }
+
+               
                return 0;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedCommand", "execute");
                exit(1);
        }
-
 }
 //**********************************************************************************************************************
 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
@@ -140,18 +155,18 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
                for (int i = 0; i < thislookup.size(); i++) {
                        out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
                        thislookup[i]->print(out);
+                       
+                       RAbundVector rav = thislookup[i]->getRAbundVector();
+                       openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+                       rav.print(*(filehandles[thislookup[i]->getGroup()]));
+                       (*(filehandles[thislookup[i]->getGroup()])).close();
                }
  
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedCommand", "printSharedData");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedCommand class function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       
 }
 
 //**********************************************************************************************************************