fixed get.lienage and remove.lineage bug with confidence scores that are floats....

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index c5e579e730e1cfbd3da0040359393ef08b497295..038460fe1485dc531cec04f83b28793f0b55a550 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -25,6 +25,7 @@ vector<string> ChimeraPintailCommand::getValidParameters(){
 //**********************************************************************************************************************
 ChimeraPintailCommand::ChimeraPintailCommand(){        
        try {
+               abort = true; calledHelp = true;
                vector<string> tempOutNames;
                outputTypes["chimera"] = tempOutNames;
                outputTypes["accnos"] = tempOutNames;
@@ -60,10 +61,10 @@ vector<string> ChimeraPintailCommand::getRequiredFiles(){
 //***************************************************************************************************************
 ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -309,7 +310,7 @@ ChimeraPintailCommand::~ChimeraPintailCommand(){    /*      do nothing      */      }
 int ChimeraPintailCommand::execute(){
        try{
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                for (int s = 0; s < fastaFileNames.size(); s++) {
                                
@@ -516,6 +517,13 @@ int ChimeraPintailCommand::execute(){
                        m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); 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); }
+               }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }