X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.cpp;h=2ce9bbcded2ba51409f9d130489953a3753ea438;hb=05a0195e07c42c996592ee1c8abb63adedb7f493;hp=9afb401014faaf097a1a30c2b1802d82ae8e659f;hpb=ac1da2a793271cb67f2a2155c5558e1fabdd6aba;p=mothur.git

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 9afb401..2ce9bbc 100644
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -51,38 +51,54 @@ int SharedCommand::execute(){
 	try {
 		
 		//lookup.clear();
-		int count = 1;
 		string errorOff = "no error";
 			
 		//read in listfile
 		read = new ReadOTUFile(globaldata->inputFileName);	
 		read->read(&*globaldata); 
+		delete read;
 
 		input = globaldata->ginput;
 		SharedList = globaldata->gSharedList;
 		string lastLabel = SharedList->getLabel();
 		vector<SharedRAbundVector*> lookup; 
-				
+		
+		if (SharedList->getNumSeqs() != groupMap->getNumSeqs()) {  
+			mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); mothurOutEndLine(); 
+			
+			out.close();
+			remove(filename.c_str()); //remove blank shared file you made
+			
+			createMisMatchFile();
+			
+			//delete memory
+			for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+				delete it3->second;
+			}
+			delete SharedList;
+			globaldata->gSharedList = NULL;
+			
+			return 1; 
+		}
+		
 		//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;
 		
 		
-		while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+		while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
 			
 
-			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+			if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
 					
 					lookup = SharedList->getSharedRAbundVector();
-					mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+					mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 					
 					printSharedData(lookup); //prints info to the .shared file
 					for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 				
 					processedLabels.insert(SharedList->getLabel());
 					userLabels.erase(SharedList->getLabel());
-					userLines.erase(count);
 			}
 			
 			if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
@@ -90,7 +106,7 @@ int SharedCommand::execute(){
 					SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 					
 					lookup = SharedList->getSharedRAbundVector();
-					mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+					mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 					
 					printSharedData(lookup); //prints info to the .shared file
 					for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
@@ -104,8 +120,6 @@ int SharedCommand::execute(){
 				
 			delete SharedList;
 			SharedList = input->getSharedListVector(); //get new list vector to process
-			
-			count++;		
 		}
 		
 		//output error messages about any remaining user labels
@@ -117,13 +131,13 @@ int SharedCommand::execute(){
 			}
 		}
 		
-		//run last line if you need to
+		//run last label if you need to
 		if (needToRun == true)  {
-			delete SharedList;
+			if (SharedList != NULL) {	delete SharedList;	}
 			SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
 					
 			lookup = SharedList->getSharedRAbundVector();
-			mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+			mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 			
 			printSharedData(lookup); //prints info to the .shared file
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
@@ -131,7 +145,6 @@ int SharedCommand::execute(){
 		}
 		
 		globaldata->gSharedList = NULL;
-		delete read;
 		
 		out.close();
 		
@@ -168,6 +181,89 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+void SharedCommand::createMisMatchFile() {
+	try {
+		ofstream outMisMatch;
+		string outputMisMatchName = getRootName(globaldata->inputFileName);
+		
+		//you have sequences in your list file that are not in your group file
+		if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) { 
+			outputMisMatchName += "missing.group";
+			mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+			
+			openOutputFile(outputMisMatchName, outMisMatch);
+			
+			//go through list and if group returns "not found" output it
+			for (int i = 0; i < SharedList->getNumBins(); i++) {
+			
+				string names = SharedList->get(i); 
+				
+				while (names.find_first_of(',') != -1) { 
+					string name = names.substr(0,names.find_first_of(','));
+					names = names.substr(names.find_first_of(',')+1, names.length());
+					string group = groupMap->getGroup(name);
+					
+					if(group == "not found") {	outMisMatch << name << endl;  }
+				}
+				
+				//get last name
+				string group = groupMap->getGroup(names);
+				if(group == "not found") {	outMisMatch << names << endl;  }				
+			}
+			
+			outMisMatch.close();
+			
+		
+		}else {//you have sequences in your group file that are not in you list file
+			
+			outputMisMatchName += "missing.name";
+			mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+			
+			map<string, string> namesInList;
+			
+			//go through listfile and get names
+			for (int i = 0; i < SharedList->getNumSeqs(); i++) {
+				
+				string names = SharedList->get(i); 
+				
+				while (names.find_first_of(',') != -1) { 
+					string name = names.substr(0,names.find_first_of(','));
+					names = names.substr(names.find_first_of(',')+1, names.length());
+					
+					namesInList[name] = name;
+				}
+				
+				//get last name
+				namesInList[names] = names;				
+			}
+			
+			//get names of sequences in groupfile
+			vector<string> seqNames = groupMap->getNamesSeqs();
+		
+			map<string, string>::iterator itMatch;
+			
+			openOutputFile(outputMisMatchName, outMisMatch);
+			
+			//loop through names in seqNames and if they aren't in namesIn list output them
+			for (int i = 0; i < seqNames.size(); i++) {
+				
+				itMatch = namesInList.find(seqNames[i]);
+				
+				if (itMatch == namesInList.end()) {
+				
+					outMisMatch << seqNames[i] << endl; 
+				}
+			}		
+			outMisMatch.close();
+		}
+ 
+	}
+	catch(exception& e) {
+		errorOut(e, "SharedCommand", "createMisMatchFile");
+		exit(1);
+	}
+}
 
 //**********************************************************************************************************************