X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.cpp;h=c49e56ac8d9264f535a7b9c6f7457948f421f69a;hb=1244c4907c07baea86b0f0676d098a29d2e95a39;hp=6ca1ed63585463d92ac8dc7aa65f921ca1070308;hpb=016a30dacbe75869aef5fdb58d2d1bf9eb8f9b33;p=mothur.git

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 6ca1ed6..c49e56a 100644
--- 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);
-	}
-	
 }
 
 //**********************************************************************************************************************