added set.current and get.current commands and modified existing commands to update...

[mothur.git] / removegroupscommand.cpp

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 4462b52863f235cb8436d0db77fe5a3698823534..34a072b30a0b563fd22ddef60099224bdc6bf9f0 100644 (file)
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -258,6 +258,33 @@ int RemoveGroupsCommand::execute(){
                        m->mothurOut("Output File names: "); m->mothurOutEndLine();
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
                        m->mothurOutEndLine();
+                       
+                       //set fasta file as new current fastafile
+                       string current = "";
+                       itTypes = outputTypes.find("fasta");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("name");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("group");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("list");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("taxonomy");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+                       }
                }
                
                return 0;