removed line option

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index aba07b2a8d97503913cff85fedde5d8562ca4f5c..c3f99d2704bec1fc11f0383a69f015768857aad2 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -51,7 +51,6 @@ int SharedCommand::execute(){
        try {
                
                //lookup.clear();
-               int count = 1;
                string errorOff = "no error";
                        
                //read in listfile
@@ -82,13 +81,12 @@ int SharedCommand::execute(){
                //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()); mothurOutEndLine();
@@ -98,7 +96,6 @@ int SharedCommand::execute(){
                                
                                        processedLabels.insert(SharedList->getLabel());
                                        userLabels.erase(SharedList->getLabel());
-                                       userLines.erase(count);
                        }
                        
                        if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
@@ -120,8 +117,6 @@ int SharedCommand::execute(){
                                
                        delete SharedList;
                        SharedList = input->getSharedListVector(); //get new list vector to process
-                       
-                       count++;                
                }
                
                //output error messages about any remaining user labels
@@ -133,7 +128,7 @@ int SharedCommand::execute(){
                        }
                }
                
-               //run last line if you need to
+               //run last label if you need to
                if (needToRun == true)  {
                        if (SharedList != NULL) {       delete SharedList;      }
                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process