X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.cpp;h=8683fc3fa80154729ea5228fcaa38fb03726603a;hb=0e40e23448c2ee274268d85e0d0e65cb9eaeee6f;hp=5b9cde8c84b10e0d4f6dd938dbf68191000930f4;hpb=284fd95c611ccc3b1a7875c4dacfca06d1f50ed6;p=mothur.git

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 5b9cde8..8683fc3 100644
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -9,6 +9,55 @@
 
 #include "readotucommand.h"
 
+//**********************************************************************************************************************
+vector<string> ReadOtuCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ReadOtuCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+ReadOtuCommand::ReadOtuCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["rabund"] = tempOutNames;
+		outputTypes["shared"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ReadOtuCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"list","shared","relabund","sabund","rabund","or"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ReadOtuCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ReadOtuCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 ReadOtuCommand::ReadOtuCommand(string option)  {
 	try {
@@ -34,7 +83,12 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 			for (it = parameters.begin(); it != parameters.end(); it++) { 
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
-	
+			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["rabund"] = tempOutNames;
+			outputTypes["shared"] = tempOutNames;
+			
 			globaldata->newRead();
 			
 			//if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -45,7 +99,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 				it = parameters.find("list");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["list"] = inputDir + it->second;		}
 				}
@@ -53,7 +107,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 				it = parameters.find("order");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["order"] = inputDir + it->second;		}
 				}
@@ -61,7 +115,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 				it = parameters.find("shared");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["shared"] = inputDir + it->second;		}
 				}
@@ -69,7 +123,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 				it = parameters.find("group");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["group"] = inputDir + it->second;		}
 				}
@@ -77,7 +131,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 				it = parameters.find("sabund");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["sabund"] = inputDir + it->second;		}
 				}
@@ -85,7 +139,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 				it = parameters.find("rabund");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["rabund"] = inputDir + it->second;		}
 				}
@@ -93,7 +147,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 				it = parameters.find("ordergroup");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["ordergroup"] = inputDir + it->second;		}
 				}
@@ -101,7 +155,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 				it = parameters.find("relabund");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["relabund"] = inputDir + it->second;		}
 				}
@@ -159,7 +213,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }
 			else { 
-				splitAtDash(groups, Groups);
+				m->splitAtDash(groups, Groups);
 				globaldata->Groups = Groups;
 			}
 
@@ -176,7 +230,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 			label = validParameter.validFile(parameters, "label", false);			
 			if (label == "not found") { label = ""; }
 			else { 
-				if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+				if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 				else { allLines = 1;  }
 				globaldata->labels = labels;
 			}
@@ -255,6 +309,8 @@ int ReadOtuCommand::execute(){
 				//m->mothurOutEndLine();
 			}
 			
+			outputTypes = shared->getOutputFiles();
+			
 			delete shared;
 		}
 		return 0;