X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.cpp;h=dd900643a741d576d1595c1a9c346d6b6c334361;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=a797d5408d151beddc73be085111bbcf41cd84cd;hpb=16bea3130e36addc54e2116dfbcd02d706ebee45;p=mothur.git

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index a797d54..dd90064 100644
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -36,26 +36,80 @@ SharedCommand::SharedCommand(){
 int SharedCommand::execute(){
 	try {
 		globaldata = GlobalData::getInstance();
+		//lookup.clear();
+		int count = 1;
+		string errorOff = "no error";
 			
 		//read in listfile
-		read = new ReadPhilFile(globaldata->inputFileName);	
+		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;
+		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 		
 		shared = new Shared();
-		int i = 0;
-		while(SharedList != NULL){
 		
-			if(globaldata->allLines == 1 || globaldata->lines.count(i+1) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+		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
+				
+					processedLabels.insert(SharedList->getLabel());
+					userLabels.erase(SharedList->getLabel());
+					userLines.erase(count);
+			}
 			
-				shared->getSharedVectors(i, SharedList); //fills sharedGroups with new info and updates sharedVector
-				printSharedData(); //prints info to the .shared file
+			if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
+					shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
+					printSharedData(); //prints info to the .shared file
+
+					processedLabels.insert(lastList->getLabel());
+					userLabels.erase(lastList->getLabel());
 			}
 			
+			if (count != 1) { delete lastList; }
+			lastList = SharedList;			
 			SharedList = input->getSharedListVector(); //get new list vector to process
-			i++;
+			
+			//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
+		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(lastList->getLabel()) != 1) {
+				//cout << ". I will use " << lastList->getLabel() << "." << endl;
+				needToRun = true;
+			}else {
+				//cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+			}
+		}
+		
+		//run last line if you need to
+		if (needToRun == true)  {
+			shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
+			printSharedData(); //prints info to the .shared file
 		}
+		
+		delete lastList;
+		delete shared;
+		out.close();
+		
 		return 0;
 	}
 	catch(exception& e) {
@@ -71,6 +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
@@ -93,6 +153,7 @@ void SharedCommand::printSharedData() {
 SharedCommand::~SharedCommand(){
 	//delete list;
 	delete read;
+	
 }
 
 //**********************************************************************************************************************