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

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 638119543480ffe0a8364379edfef0b184c526bf..17258159b7562dbee9830a03746602d935bb43a6 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -34,6 +34,53 @@
 #include "solow.h"
 #include "shen.h"
 
+//**********************************************************************************************************************
+vector<string> SummaryCommand::getValidParameters(){   
+       try {
+               string Array[] =  {"label","calc","abund","size","outputdir","groupmode","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SummaryCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+SummaryCommand::SummaryCommand(){      
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["summary"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SummaryCommand", "SummaryCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SummaryCommand::getRequiredParameters(){        
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SummaryCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SummaryCommand::getRequiredFiles(){     
+       try {
+               string AlignArray[] =  {"shared","list","rabund","sabund","or"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SummaryCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 SummaryCommand::SummaryCommand(string option)  {
@@ -62,6 +109,10 @@ SummaryCommand::SummaryCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["summary"] = tempOutNames;
+                       
                        //make sure the user has already run the read.otu command
                        if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the summary.single command."); m->mothurOutEndLine(); abort = true; }
                        
@@ -144,8 +195,6 @@ int SummaryCommand::execute(){
        
                if (abort == true) { return 0; }
                
-               vector<string> outputNames;
-               
                string hadShared = "";
                if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
                else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
@@ -162,7 +211,7 @@ int SummaryCommand::execute(){
                        
                        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
                        globaldata->inputFileName = inputFileNames[p];
-                       outputNames.push_back(fileNameRoot);
+                       outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
                        
                        if (inputFileNames.size() > 1) {
                                m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();