added get.rabund and get.sabund command and fixed bug introduced by line by line...

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 7f97ef3e31bb802b01aa0f86eb2262c50b230ac8..850df46929f8b4f7efa076a17b0052136f204b23 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -329,9 +329,10 @@ void TreeGroupCommand::makeSimsShared() {
                
                set<string> processedLabels;
                set<string> userLabels = globaldata->labels;
+               set<int> userLines = globaldata->lines;
 
                //as long as you are not at the end of the file or done wih the lines you want
-               while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+               while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
                
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){                   
                                cout << lookup[0]->getLabel() << '\t' << count << endl;
@@ -339,6 +340,7 @@ void TreeGroupCommand::makeSimsShared() {
                                
                                processedLabels.insert(lookup[0]->getLabel());
                                userLabels.erase(lookup[0]->getLabel());
+                               userLines.erase(count);
                        }
                        
                        if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {