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

[mothur.git] / clusterfragmentscommand.cpp

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 24070d2bb0e8b8f781eece4e35e7dec4f42d6797..be78e76d75e15ace53867afb13bece32969c76ad 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -40,8 +40,7 @@ vector<string> ClusterFragmentsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClusterFragmentsCommand::ClusterFragmentsCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["name"] = tempOutNames;
@@ -77,10 +76,10 @@ vector<string> ClusterFragmentsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 ClusterFragmentsCommand::ClusterFragmentsCommand(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
@@ -182,7 +181,7 @@ void ClusterFragmentsCommand::help(){
 int ClusterFragmentsCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                int start = time(NULL);
                
@@ -259,6 +258,18 @@ int ClusterFragmentsCommand::execute(){
                m->mothurOut(newNamesFile); m->mothurOutEndLine();      
                outputNames.push_back(newFastaFile);  outputNames.push_back(newNamesFile); outputTypes["fasta"].push_back(newFastaFile); outputTypes["name"].push_back(newNamesFile);
                m->mothurOutEndLine();
+               
+               //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); }
+               }
 
                return 0;