added multiple processors option for Windows users to align.seqs, dist.seqs, summary...

[mothur.git] / sensspeccommand.cpp

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index c7f67b40b0e10ae14741600f9b8b3b8d7e0adaa2..726c9045b20dfd7ac907b5e73f0692e3d0835c69 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -66,6 +66,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        string temp;
@@ -133,16 +134,17 @@ SensSpecCommand::SensSpecCommand(string option)  {
                                else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (listFile == "not open") { abort = true; }      
+                       else { m->setListFile(listFile); }
                        
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not found") { phylipfile = "";  }
                        else if (phylipfile == "not open") { abort = true; }    
-                       else { distFile = phylipfile; format = "phylip";   }
+                       else { distFile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile);  }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not found") { columnfile = ""; }
                        else if (columnfile == "not open") { abort = true; }    
-                       else { distFile = columnfile; format = "column";   }
+                       else { distFile = columnfile; format = "column";   m->setColumnFile(columnfile); }
                        
                        if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
                                //give priority to column, then phylip
@@ -189,7 +191,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
                        
                        lineLabel = validParameter.validFile(parameters, "label", false);       if (lineLabel == "not found") { lineLabel = ""; }
                        
-                       sensSpecFileName = listFile.substr(0,listFile.find_last_of('.')) + ".sensspec";
+                       sensSpecFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + ".sensspec";
                }
        }
        catch(exception& e) {