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

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index a8ca812e0e0cb6854fd3c806e8e26249eb9400a2..bdfbeae8f845fc235ac3d115367a13ac61ff883e 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -24,8 +24,7 @@ vector<string> SplitAbundCommand::getValidParameters(){
 //**********************************************************************************************************************
 SplitAbundCommand::SplitAbundCommand(){        
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;
                outputTypes["name"] = tempOutNames;
@@ -64,11 +63,11 @@ vector<string> SplitAbundCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 SplitAbundCommand::SplitAbundCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                        
                //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
@@ -233,7 +232,7 @@ SplitAbundCommand::~SplitAbundCommand(){
 int SplitAbundCommand::execute(){
        try {
        
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                if (listfile != "") { //you are using a listfile to determine abundance
                        if (outputDir == "") { outputDir = m->hasPath(listfile); }
@@ -333,6 +332,33 @@ int SplitAbundCommand::execute(){
                        if (fastafile != "")                            {  parseFasta(tag);             }
                }
                
+               //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("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();    }