fixed bug in bootstrap command that was caused by globaldata's breakup, and made...

[mothur.git] / concensuscommand.cpp

diff --git a/concensuscommand.cpp b/concensuscommand.cpp
index 30da32cfe05db5de942cebd213cf9cc9631cb717..37609c3fb4858ca32c02be71539da5547a4c909c 100644 (file)
--- a/concensuscommand.cpp
+++ b/concensuscommand.cpp
@@ -11,21 +11,24 @@
 
 //**********************************************************************************************************************
 
-ConcensusCommand::ConcensusCommand(string option){
+ConcensusCommand::ConcensusCommand(string fileroot){
        try {
                globaldata = GlobalData::getInstance();
                abort = false;
                
+               filename = fileroot;
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               //if(option == "help") { help(); abort = true; }
                
-               else {
-                       if (option != "") { mothurOut("There are no valid parameters for the concensus command."); mothurOutEndLine(); abort = true; }
+               //else {
+                       //if (option != "") { mothurOut("There are no valid parameters for the concensus command."); mothurOutEndLine(); abort = true; }
                        
-                       //no trees were read
-                       if (globaldata->gTree.size() == 0) {  mothurOut("You must execute the read.tree command, before you may use the concensus command."); mothurOutEndLine(); abort = true;  }
-                       else {  t = globaldata->gTree;  }
-               }
+               //      //no trees were read
+               //      if (globaldata->gTree.size() == 0) {  mothurOut("You must execute the read.tree command, before you may use the concensus command."); mothurOutEndLine(); abort = true;  }
+                       //else { 
+                        t = globaldata->gTree;
+                        //     }
+               //}
        }
        catch(exception& e) {
                errorOut(e, "ConcensusCommand", "ConcensusCommand");
@@ -71,7 +74,7 @@ int ConcensusCommand::execute(){
                getSets();              
                
                //open file for pairing not included in the tree
-               notIncluded = getRootName(globaldata->inputFileName) + "concensuspairs";
+               notIncluded = filename + ".concensuspairs";
                openOutputFile(notIncluded, out2);
                
                concensusTree = new Tree();
@@ -140,7 +143,7 @@ int ConcensusCommand::execute(){
                        out2 << '\t' << it2->second << endl;
                }
                
-               outputFile = getRootName(globaldata->inputFileName) + "concensus.tre";
+               outputFile = filename + ".cons.tre";
                openOutputFile(outputFile, out);
                
                concensusTree->printForBoot(out);