X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=7ad41367f795abe7aeeda1052a8211daf72aeaf4;hb=d205e70ae86dbee2efc2df02f2717975854de6ba;hp=89ab0a49a7592a86638d801aaaf0257f63a34379;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 89ab0a4..7ad4136 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -44,7 +44,7 @@ vector<string> CollectCommand::setParameters(){
 		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
 		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
 		CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
-		CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-np_shannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
+		CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
 		CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
 		CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
@@ -94,7 +94,7 @@ CollectCommand::CollectCommand(){
 		outputTypes["jack"] = tempOutNames;
 		outputTypes["shannon"] = tempOutNames;
 		outputTypes["shannoneven"] = tempOutNames;
-		outputTypes["np_shannon"] = tempOutNames;
+		outputTypes["npshannon"] = tempOutNames;
 		outputTypes["heip"] = tempOutNames;
 		outputTypes["smithwilson"] = tempOutNames;
 		outputTypes["simpson"] = tempOutNames;
@@ -151,7 +151,7 @@ CollectCommand::CollectCommand(string option)  {
 			outputTypes["jack"] = tempOutNames;
 			outputTypes["shannon"] = tempOutNames;
 			outputTypes["shannoneven"] = tempOutNames;
-			outputTypes["np_shannon"] = tempOutNames;
+			outputTypes["npshannon"] = tempOutNames;
 			outputTypes["heip"] = tempOutNames;
 			outputTypes["smithwilson"] = tempOutNames;
 			outputTypes["simpson"] = tempOutNames;
@@ -280,13 +280,13 @@ CollectCommand::CollectCommand(string option)  {
 
 			string temp;
 			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, freq); 
+			m->mothurConvert(temp, freq); 
 			
 			temp = validParameter.validFile(parameters, "abund", false);		if (temp == "not found") { temp = "10"; }
-			convert(temp, abund); 
+			m->mothurConvert(temp, abund); 
 			
 			temp = validParameter.validFile(parameters, "size", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, size); 
+			m->mothurConvert(temp, size); 
 		}
 		
 	}
@@ -307,7 +307,7 @@ int CollectCommand::execute(){
 	
 		for (int p = 0; p < inputFileNames.size(); p++) {
 			
-			if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}  m->Groups.clear();  return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}  m->clearGroups();  return 0; }
 			
 			if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
 			string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
@@ -346,8 +346,8 @@ int CollectCommand::execute(){
 						cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
 						outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven");
 					}else if (Estimators[i] == "npshannon") { 
-						cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
-						outputNames.push_back(fileNameRoot+"np_shannon"); outputTypes["np_shannon"].push_back(fileNameRoot+"np_shannon");
+						cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"npshannon")));
+						outputNames.push_back(fileNameRoot+"npshannon"); outputTypes["npshannon"].push_back(fileNameRoot+"npshannon");
 					}else if (Estimators[i] == "heip") { 
 						cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
 						outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");
@@ -416,7 +416,7 @@ int CollectCommand::execute(){
 				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} outputTypes.clear(); 
 				delete input;  
 				delete order; 
-				m->Groups.clear();
+				m->clearGroups();
 				return 0;
 			}
 
@@ -428,7 +428,7 @@ int CollectCommand::execute(){
 					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} outputTypes.clear(); 
 					delete input;  
 					delete order; 
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 				}
 
@@ -476,7 +476,7 @@ int CollectCommand::execute(){
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
 					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} outputTypes.clear(); 
 					delete input;  
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 			}
 				
@@ -509,7 +509,7 @@ int CollectCommand::execute(){
 					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} outputTypes.clear(); 
 					delete input;  
 					delete order;
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 				}
 				delete order;