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

[mothur.git] / subsamplecommand.cpp

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 223c9f5edf68c6eaa23f668e48ac0917854f6067..d24bcc5ad616b324b444f929ec3be57716dd05de 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -295,7 +295,44 @@ int SubSampleCommand::execute(){
                if (fastafile != "")    {   getSubSampleFasta();        }
                if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }
                        
-                               
+               //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("shared");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+               }
+               
+               itTypes = outputTypes.find("rabund");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+               }
+               
+               itTypes = outputTypes.find("sabund");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
+               }
+               
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }