X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.cpp;h=2c1b6af3004e7351085e4538f7023e342bc181f9;hb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;hp=91bb8e19604d3d9446016c4b9eaf82f566172c0a;hpb=762b3e4c83e1e8e8392c1199b6482d36ee89e50f;p=mothur.git

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 91bb8e1..2c1b6af 100644
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -21,12 +21,12 @@ SharedCommand::SharedCommand(string o) : outputDir(o) {
 		
 		//getting output filename
 		filename = globaldata->inputFileName;
-		if (outputDir == "") { outputDir += hasPath(filename); }
+		if (outputDir == "") { outputDir += m->hasPath(filename); }
 		
-		filename = outputDir + getRootName(getSimpleName(filename));
+		filename = outputDir + m->getRootName(m->getSimpleName(filename));
 		filename = filename + "shared";
 		
-		openOutputFile(filename, out);
+		m->openOutputFile(filename, out);
 		pickedGroups = false;
 		
 		groupMap = globaldata->gGroupmap;
@@ -48,7 +48,7 @@ SharedCommand::SharedCommand(string o) : outputDir(o) {
 		}
 		
 		//set fileroot
-		fileroot = outputDir + getRootName(getSimpleName(globaldata->getListFile()));
+		fileroot = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile()));
 		
 		//clears file before we start to write to it below
 		for (int i=0; i<groups.size(); i++) {
@@ -71,6 +71,9 @@ int SharedCommand::execute(){
 		string errorOff = "no error";
 		//errorOff = "";
 		
+		//if user provided an order file containing the order the shared file should be in read it
+		if (globaldata->getOrderGroupFile() != "") { readOrderFile(); }
+		
 		//read in listfile
 		read = new ReadOTUFile(globaldata->inputFileName);	
 		read->read(&*globaldata); 
@@ -116,9 +119,9 @@ int SharedCommand::execute(){
 				groups += globaldata->Groups[i] + ".";
 			}
 		
-			string newGroupFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + groups + "groups";
+			string newGroupFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + groups + "groups";
 			ofstream outGroups;
-			openOutputFile(newGroupFile, outGroups);
+			m->openOutputFile(newGroupFile, outGroups);
 		
 			vector<string> names = groupMap->getNamesSeqs();
 			string groupName;
@@ -169,7 +172,7 @@ int SharedCommand::execute(){
 					userLabels.erase(SharedList->getLabel());
 			}
 			
-			if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+			if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
 					string saveLabel = SharedList->getLabel();
 					
 					delete SharedList;
@@ -280,18 +283,46 @@ int SharedCommand::execute(){
 void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
 	try {
 		
-		sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
-		
-		//initialize bin values
-		for (int i = 0; i < thislookup.size(); i++) {
-//cout << "in printData " << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() <<  endl;
-			out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
-			thislookup[i]->print(out);
+		if (order.size() == 0) { //user has not specified an order so do aplabetically
+			sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
+			
+			//initialize bin values
+			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();
+				m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+				rav.print(*(filehandles[thislookup[i]->getGroup()]));
+				(*(filehandles[thislookup[i]->getGroup()])).close();
+			}
+		}else{
+			//create a map from groupName to each sharedrabund
+			map<string, SharedRAbundVector*> myMap;
+			map<string, SharedRAbundVector*>::iterator myIt;
+			
+			for (int i = 0; i < thislookup.size(); i++) {
+				myMap[thislookup[i]->getGroup()] = thislookup[i];
+			}
+			
 			
-			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();
+			//loop through ordered list and print the rabund
+			for (int i = 0; i < order.size(); i++) {
+				myIt = myMap.find(order[i]);
+				
+				if(myIt != myMap.end()) { //we found it
+					out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
+					(myIt->second)->print(out);
+				
+					RAbundVector rav = (myIt->second)->getRAbundVector();
+					m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
+					rav.print(*(filehandles[(myIt->second)->getGroup()]));
+					(*(filehandles[(myIt->second)->getGroup()])).close();
+				}else{
+					m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
+				}
+			}
+		
 		}
  
 	}
@@ -346,14 +377,14 @@ int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 int SharedCommand::createMisMatchFile() {
 	try {
 		ofstream outMisMatch;
-		string outputMisMatchName = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+		string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
 		
 		//you have sequences in your list file that are not in your group file
 		if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) { 
 			outputMisMatchName += "missing.group";
 			m->mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
 			
-			openOutputFile(outputMisMatchName, outMisMatch);
+			m->openOutputFile(outputMisMatchName, outMisMatch);
 			
 			map<string, string> listNames;
 			map<string, string>::iterator itList;
@@ -427,7 +458,7 @@ int SharedCommand::createMisMatchFile() {
 		
 			map<string, string>::iterator itMatch;
 			
-			openOutputFile(outputMisMatchName, outMisMatch);
+			m->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++) {
@@ -458,7 +489,32 @@ SharedCommand::~SharedCommand(){
 	
 	
 }
-
+//**********************************************************************************************************************
+int SharedCommand::readOrderFile() {
+	try {
+		//remove old names
+		order.clear();
+		
+		ifstream in;
+		m->openInputFile(globaldata->getOrderGroupFile(), in);
+		string thisGroup;
+		
+		while(!in.eof()){
+			in >> thisGroup; m->gobble(in);
+						
+			order.push_back(thisGroup);
+			
+			if (m->control_pressed) { order.clear(); break; }
+		}
+		in.close();		
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedCommand", "readOrderFile");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {