minor bugs fixes and added line and label options to read.otu's parselist and shared...

[mothur.git] / parselistcommand.cpp

diff --git a/parselistcommand.cpp b/parselistcommand.cpp
index 5379052d6dd4f1bbfe51b3b346874def78a7b841..d9925ad40ecd02cc1580e7d087b6b5acb3514831 100644 (file)
--- a/parselistcommand.cpp
+++ b/parselistcommand.cpp
@@ -86,6 +86,7 @@ void ParseListCommand::parse(int index) {
 int ParseListCommand::execute(){
        try{
                        globaldata = GlobalData::getInstance();
+                       int count = 1;
                        
                        //read in listfile
                        read = new ReadPhilFile(globaldata->inputFileName);     
@@ -107,22 +108,30 @@ int ParseListCommand::execute(){
                        //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->getSharedListVector();
+                               count++;
                        }
                        
                        //set groupmap for .shared commands