working on pca

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 360e1955bab31055c4ad06f71c933a4228058386..a8a9d2b5a6cff6da2ab8e86e22af19782f5ce0bf 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -226,6 +226,7 @@ int ListSeqsCommand::execute(){
 
                ofstream out;
                m->openOutputFile(outputFileName, out);
+               outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
                
                //output to .accnos file
                for (int i = 0; i < names.size(); i++) {
@@ -237,12 +238,21 @@ int ListSeqsCommand::execute(){
                out.close();
                
                if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0; }
-
+               
+               m->setAccnosFile(outputFileName);
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-               m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
+               m->mothurOut(outputFileName); m->mothurOutEndLine();    
                m->mothurOutEndLine();
                
+               //set accnos file as new current accnosfile
+               string current = "";
+               itTypes = outputTypes.find("accnos");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+               }
+               
                return 0;               
        }
 
@@ -259,7 +269,7 @@ int ListSeqsCommand::readFasta(){
                ifstream in;
                m->openInputFile(fastafile, in);
                string name;
-       
+               
                while(!in.eof()){
                        
                        if (m->control_pressed) { in.close(); return 0; }
@@ -444,6 +454,7 @@ int ListSeqsCommand::readTax(){
                        names.push_back(firstCol);
                        
                        m->gobble(in);
+                       
                }
                in.close();