X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getgroupcommand.cpp;h=529ed934d5b194d1a1d82869c44053ca4f7bbaf2;hp=ce3cf73d28e455fd3b111f3a10b7e74ba7f67186;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index ce3cf73..529ed93 100644
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -8,13 +8,14 @@
  */
 
 #include "getgroupcommand.h"
+#include "inputdata.h"
 
 //**********************************************************************************************************************
 vector<string> GetgroupCommand::setParameters(){	
 	try {
-		CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none",false,true); parameters.push_back(pshared);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none","",false,true, true); parameters.push_back(pshared);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -30,7 +31,6 @@ string GetgroupCommand::getHelpString(){
 	try {
 		string helpString = "";
 		helpString += "The get.group command parameter is shared and it's required if you have no valid current file.\n";
-		//m->mothurOut("The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the consensus command.\n");
 		helpString += "You may not use any parameters with the get.group command.\n";
 		helpString += "The get.group command should be in the following format: \n";
 		helpString += "get.group()\n";
@@ -42,13 +42,12 @@ string GetgroupCommand::getHelpString(){
 		exit(1);
 	}
 }
+
 //**********************************************************************************************************************
 GetgroupCommand::GetgroupCommand(){	
 	try {
 		abort = true; calledHelp = true; 
 		setParameters();
-		vector<string> tempOutNames;
-		outputTypes["bootgroup"] = tempOutNames;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
@@ -62,11 +61,10 @@ GetgroupCommand::GetgroupCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
-			//valid paramters for this command
-			string Array[] =  {"outputdir","inputdir"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string,string> parameters = parser.getParameters();
@@ -78,10 +76,6 @@ GetgroupCommand::GetgroupCommand(string option)  {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
-			//initialize outputTypes
-			vector<string> tempOutNames;
-			outputTypes["bootgroup"] = tempOutNames;
-			
 			//if the user changes the input directory command factory will send this info to us in the output parameter 
 			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
 			if (inputDir == "not found"){	inputDir = "";		}
@@ -104,7 +98,7 @@ GetgroupCommand::GetgroupCommand(string option)  {
 				sharedfile = m->getSharedFile(); 
 				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}
+			}else { m->setSharedFile(sharedfile); }
 			
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -122,62 +116,17 @@ int GetgroupCommand::execute(){
 	try {
 	
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+					
+		InputData input(sharedfile, "sharedfile");
+		vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 		
-		//open shared file
-		m->openInputFile(sharedfile, in);
-			
-		//open output file
-		outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
-		m->openOutputFile(outputFile, out);
-			
-		int num, inputData, count;
-		count = 0;  
-		string holdLabel, nextLabel, groupN, label;
-		
-		//read in first row since you know there is at least 1 group.
-		in >> label >> groupN >> num;
-		holdLabel = label;
-		
-		//output first group
-		m->mothurOut(groupN); m->mothurOutEndLine();
-		out << groupN << '\t' << groupN << endl;	
-			
-		//get rest of line
-		for(int i=0;i<num;i++){
-			in >> inputData;
+		for (int i = 0; i < lookup.size(); i++) {
+			m->mothurOut(lookup[i]->getGroup()); m->mothurOutEndLine();
+			delete lookup[i];
 		}
-		
-		if (m->control_pressed) { outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
-
-		if (in.eof() != true) { in >> nextLabel; }
-		
-		//read the rest of the groups info in
-		while ((nextLabel == holdLabel) && (in.eof() != true)) {
-			if (m->control_pressed) {  outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
-			
-			in >> groupN >> num;
-			count++;
-			
-			//output next group
-			m->mothurOut(groupN); m->mothurOutEndLine();
-			out << groupN << '\t' << groupN << endl;				
-			
-			//fill vector.  
-			for(int i=0;i<num;i++){
-				in >> inputData;
-			}
 			
-			if (in.eof() != true) { in >> nextLabel; }
-		}
-		
-		in.close();
-		out.close();
-		
-		if (m->control_pressed) {  remove(outputFile.c_str());   return 0; }
-		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-		m->mothurOut(outputFile); m->mothurOutEndLine();	outputNames.push_back(outputFile); outputTypes["bootgroup"].push_back(outputFile);
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		m->mothurOutEndLine();
 		
 		return 0;	
@@ -188,5 +137,6 @@ int GetgroupCommand::execute(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************