added pipeline commands which involved change to command factory and command class...

[mothur.git] / bootstrapsharedcommand.cpp

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index 9424347180c7713c6b498fd16cada4e7e86accd4..2b7232db4dd050a663c3a5b9514b59ae058e5c4c 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -19,9 +19,54 @@
 #include "sharedmorisitahorn.h"
 #include "sharedbraycurtis.h"
 
-
 //**********************************************************************************************************************
-
+vector<string> BootSharedCommand::getValidParameters(){        
+       try {
+               string AlignArray[] =  {"label","calc","groups","iters","outputdir","inputdir"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BootSharedCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+BootSharedCommand::BootSharedCommand(){        
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["tree"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BootSharedCommand", "BootSharedCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> BootSharedCommand::getRequiredParameters(){     
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BootSharedCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> BootSharedCommand::getRequiredFiles(){  
+       try {
+               string AlignArray[] =  {"shared"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BootSharedCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 BootSharedCommand::BootSharedCommand(string option) {
        try {
                globaldata = GlobalData::getInstance();
@@ -49,6 +94,10 @@ BootSharedCommand::BootSharedCommand(string option) {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["tree"] = tempOutNames;
+               
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
@@ -410,7 +459,7 @@ int BootSharedCommand::process(SharedOrderVector* order) {
                                        //create a new filename
                                        outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
                                        m->openOutputFile(outputFile, *(out[z]));
-                                       outputNames.push_back(outputFile);
+                                       outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
                                }
                                
                                m->mothurOut("Generating bootstrap trees..."); cout.flush();