X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=3541e00d064233c4da10619789291222290b33f1;hb=3114ad297d40ecd47bd3c1fe7997bd76a81e8c75;hp=bc2dd481e5589ea5ba8b319aa707ecf3a3eea463;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index bc2dd48..3541e00 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -125,9 +125,15 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
 			}
 			
 			oldNameMapFName = validParameter.validFile(parameters, "name", true);
-			if (oldNameMapFName == "not open") { abort = true; }
+			if (oldNameMapFName == "not open") { oldNameMapFName = ""; abort = true; }
 			else if (oldNameMapFName == "not found"){	oldNameMapFName = "";	}
 			else { m->setNameFile(oldNameMapFName); }
+			
+			if (oldNameMapFName == "") {
+				vector<string> files; files.push_back(inFastaName);
+				parser.getNameFile(files);
+			}
+			
 		}
 
 	}
@@ -162,6 +168,7 @@ int DeconvoluteCommand::execute() {
 		map<string, string>::iterator itStrings;
 		set<string> nameInFastaFile; //for sanity checking
 		set<string>::iterator itname;
+		vector<string> nameFileOrder;
 		int count = 0;
 		while (!in.eof()) {
 			
@@ -189,8 +196,9 @@ int DeconvoluteCommand::execute() {
 							m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine();
 						}else {
 							sequenceStrings[seq.getAligned()] = itNames->second;
+							nameFileOrder.push_back(seq.getAligned());
 						}
-					}else {	sequenceStrings[seq.getAligned()] = seq.getName();	}
+					}else {	sequenceStrings[seq.getAligned()] = seq.getName();	nameFileOrder.push_back(seq.getAligned()); }
 				}else { //this is a dup
 					if (oldNameMapFName != "") {
 						itNames = nameMap.find(seq.getName());
@@ -222,17 +230,22 @@ int DeconvoluteCommand::execute() {
 		ofstream outNames;
 		m->openOutputFile(outNameFile, outNames);
 		
-		for (itStrings = sequenceStrings.begin(); itStrings != sequenceStrings.end(); itStrings++) {
+		for (int i = 0; i < nameFileOrder.size(); i++) {
+		//for (itStrings = sequenceStrings.begin(); itStrings != sequenceStrings.end(); itStrings++) {
 			if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); outNames.close(); m->mothurRemove(outNameFile); return 0; }
 			
-			//get rep name
-			int pos = (itStrings->second).find_first_of(',');
+			itStrings = sequenceStrings.find(nameFileOrder[i]);
 			
-			if (pos == string::npos) { // only reps itself
-				outNames << itStrings->second << '\t' << itStrings->second << endl;
-			}else {
-				outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl;
-			}
+			if (itStrings != sequenceStrings.end()) {
+				//get rep name
+				int pos = (itStrings->second).find_first_of(',');
+			
+				if (pos == string::npos) { // only reps itself
+					outNames << itStrings->second << '\t' << itStrings->second << endl;
+				}else {
+					outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl;
+				}
+			}else{ m->mothurOut("[ERROR]: mismatch in namefile print."); m->mothurOutEndLine(); m->control_pressed = true; }
 		}
 		outNames.close();