fixed unifrac.weighted

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 70470b015684b386947056686789da5077000565..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; }
                        
@@ -100,7 +151,7 @@ SummaryCommand::SummaryCommand(string option)  {
                        temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
                        convert(temp, size); 
                        
-                       temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "F"; }
+                       temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
                        groupMode = m->isTrue(temp);
                        
        
@@ -123,7 +174,7 @@ void SummaryCommand::help(){
                m->mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
                validCalculator->printCalc("summary", cout);
                m->mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
-               m->mothurOut("If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=False).\n");
+               m->mothurOut("If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=true).\n");
                m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
        }
@@ -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();
@@ -445,7 +494,7 @@ vector<string> SummaryCommand::parseSharedFile(string filename) {
        }
 }
 //**********************************************************************************************************************
-string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string> outputNames) {
+string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
        try {
                
                ofstream out;
@@ -501,7 +550,9 @@ string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<
                }       
                
                //close each groups summary file
-               for (int i=0; i<outputNames.size(); i++) {  (*(filehandles[outputNames[i]])).close();  }
+               for (int i=0; i<outputNames.size(); i++) {  (*(filehandles[outputNames[i]])).close();  remove(outputNames[i].c_str());  }
+               outputNames.clear();
+               
                out.close();
                
                //return combine file name