added hcluster command and fixed some bugs, namely one with smart distancing.

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 3def8bc54f8b5a448a2023fb708eccd4e7f086f9..56f030d235212dec72677e15431fef6a6edbcad9 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -92,7 +92,7 @@ void GetSharedOTUCommand::help(){
                mothurOut("With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n");
                mothurOut("The get.sharedotu command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n");
                mothurOut("The get.sharedotu command should be in the following format: get.sabund(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n");
-               mothurOut("Example get.sharedotu(label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n");
+               mothurOut("Example get.sharedotu(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n");
                mothurOut("The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n");
                mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
        }
@@ -161,12 +161,16 @@ int GetSharedOTUCommand::execute(){
                        }
                        
                        if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                                       string saveLabel = list->getLabel();
                                        
                                        mothurOut(lastlist->getLabel()); 
                                        process(lastlist);
                                        
                                        processedLabels.insert(lastlist->getLabel());
                                        userLabels.erase(lastlist->getLabel());
+                                       
+                                       //restore real lastlabel to save below
+                                       list->setLabel(saveLabel);
                        }
 
                        lastLabel = list->getLabel();