X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistcommand.cpp;h=d9925ad40ecd02cc1580e7d087b6b5acb3514831;hb=cfb66eb46a9678a751a8f21f3ea740dffd525f5e;hp=8a848e768fd5c4c2775bec636be6acf64dd5d2ac;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/parselistcommand.cpp b/parselistcommand.cpp
index 8a848e7..d9925ad 100644
--- a/parselistcommand.cpp
+++ b/parselistcommand.cpp
@@ -27,12 +27,7 @@ ParseListCommand::ParseListCommand(){
 		}
 		
 		//set fileroot
-		if(globaldata->getFileRoot() != ""){
-			fileroot = globaldata->getFileRoot();
-		}
-		else{
-			fileroot = getRootName(globaldata->getDistFile());
-		}
+		fileroot = getRootName(globaldata->getListFile());
 		
 		//open output list files
 		for (i=0; i<groupMap->getNumGroups(); i++) {//opens an output file for each group
@@ -91,13 +86,13 @@ void ParseListCommand::parse(int index) {
 int ParseListCommand::execute(){
 	try{
 			globaldata = GlobalData::getInstance();
+			int count = 1;
 			
 			//read in listfile
 			read = new ReadPhilFile(globaldata->inputFileName);	
 			read->read(&*globaldata); 
 			input = globaldata->ginput;
-			//list = input->getListVector();
-			list = globaldata->glist;
+			list = globaldata->gSharedList;
 
 			//read in group map info.
 			groupMap = new GroupMap(globaldata->getGroupFile());
@@ -107,29 +102,41 @@ int ParseListCommand::execute(){
 			int i;
 			//create new list vectors to fill with parsed data
 			for (i=0; i<groupMap->getNumGroups(); i++) {
-				groupOfLists[groupMap->namesOfGroups[i]] = new ListVector();
+				groupOfLists[groupMap->namesOfGroups[i]] = new SharedListVector();
 			}
 			
 			//parses and sets each groups listvector
 			while(list != NULL){
 				label = list->getLabel();
-				for(i=0; i<list->size(); i++) {
-					parse(i); //parses data[i] list of sequence names
-					for (it=listGroups.begin(); it != listGroups.end(); it++) {  //loop through map and set new list vectors
-						seq = it->second;
-						seq = seq.substr(1, seq.length()); //rips off extra comma
-						groupOfLists[it->first]->push_back(seq); //sets new listvector for each group
+				
+				if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(label) == 1){
+				
+					for(i=0; i<list->size(); i++) {
+						parse(i); //parses data[i] list of sequence names
+						for (it=listGroups.begin(); it != listGroups.end(); it++) {  //loop through map and set new list vectors
+							seq = it->second;
+							seq = seq.substr(1, seq.length()); //rips off extra comma
+							groupOfLists[it->first]->push_back(seq); //sets new listvector for each group
+						}
+						listGroups.clear();
 					}
-					listGroups.clear();
-				}
-				//prints each new list file
-				for (i=0; i<groupMap->getNumGroups(); i++) {
-					groupOfLists[groupMap->namesOfGroups[i]]->setLabel(label);
-					groupOfLists[groupMap->namesOfGroups[i]]->print(*(filehandles[groupMap->namesOfGroups[i]]));
-					groupOfLists[groupMap->namesOfGroups[i]]->clear();
+					//prints each new list file
+					for (i=0; i<groupMap->getNumGroups(); i++) {
+						groupOfLists[groupMap->namesOfGroups[i]]->setLabel(label);
+						groupOfLists[groupMap->namesOfGroups[i]]->print(*(filehandles[groupMap->namesOfGroups[i]]));
+						groupOfLists[groupMap->namesOfGroups[i]]->clear();
+					}
+					
+					cout << label << '\t' << count << endl;
 				}
-				list = input->getListVector();
+				
+				list = input->getSharedListVector();
+				count++;
 			}
+			
+			//set groupmap for .shared commands
+			globaldata->gGroupmap = groupMap; 
+			
 			return 0;
 	}
 	catch(exception& e) {
@@ -146,7 +153,6 @@ int ParseListCommand::execute(){
 
 ParseListCommand::~ParseListCommand(){
 	delete list;
-	delete groupMap;
 	delete input;
 	delete read;	
 }