X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectsharedcommand.cpp;h=f3a320b89e0695483a5124b6336d68cf89179293;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=46f49b28f7b2de79b6525c05b2110325684194da;hpb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;p=mothur.git

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 46f49b2..f3a320b 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -57,7 +57,7 @@ vector<string> CollectSharedCommand::setParameters(){
 		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); 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", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-skulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
+		CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
 		CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall);
 		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
@@ -119,7 +119,7 @@ CollectSharedCommand::CollectSharedCommand(){
 		outputTypes["sharednseqs"] = tempOutNames;
 		outputTypes["ochiai"] = tempOutNames;
 		outputTypes["anderberg"] = tempOutNames;
-		outputTypes["skulczynski"] = tempOutNames;
+		outputTypes["kulczynski"] = tempOutNames;
 		outputTypes["kulczynskicody"] = tempOutNames;
 		outputTypes["lennon"] = tempOutNames;
 		outputTypes["morisitahorn"] = tempOutNames;
@@ -191,7 +191,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
 			outputTypes["sharednseqs"] = tempOutNames;
 			outputTypes["ochiai"] = tempOutNames;
 			outputTypes["anderberg"] = tempOutNames;
-			outputTypes["skulczynski"] = tempOutNames;
+			outputTypes["kulczynski"] = tempOutNames;
 			outputTypes["kulczynskicody"] = tempOutNames;
 			outputTypes["lennon"] = tempOutNames;
 			outputTypes["morisitahorn"] = tempOutNames;
@@ -238,7 +238,7 @@ CollectSharedCommand::CollectSharedCommand(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 
@@ -270,11 +270,11 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
 			else { 
 				m->splitAtDash(groups, Groups);
 			}
-			m->Groups = Groups;
+			m->setGroups(Groups);
 			
 			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, "all", false);				if (temp == "not found") { temp = "false"; }
 			all = m->isTrue(temp);
@@ -335,7 +335,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
 						}else if (Estimators[i] == "anderberg") { 
 							cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
 							outputNames.push_back(fileNameRoot+"anderberg"); outputTypes["anderberg"].push_back(fileNameRoot+"anderberg");
-						}else if (Estimators[i] == "skulczynski") { 
+						}else if (Estimators[i] == "kulczynski") { 
 							cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
 							outputNames.push_back(fileNameRoot+"kulczynski"); outputTypes["kulczynski"].push_back(fileNameRoot+"kulczynski");
 						}else if (Estimators[i] == "kulczynskicody") { 
@@ -440,15 +440,19 @@ int CollectSharedCommand::execute(){
 			
 		//set users groups
 		SharedUtil* util = new SharedUtil();
-		util->setGroups(m->Groups, m->namesOfGroups, "collect");
+		Groups = m->getGroups();
+		vector<string> allGroups = m->getAllGroups();
+		util->setGroups(Groups, allGroups, "collect");
+		m->setGroups(Groups);
+		m->setAllGroups(allGroups);
 		delete util;
 
 		while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			if (m->control_pressed) { 
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}  outputTypes.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}  outputTypes.clear();
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
 					delete order; delete input;
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 			}
 
@@ -493,9 +497,9 @@ int CollectSharedCommand::execute(){
 		}
 		
 		if (m->control_pressed) { 
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}   outputTypes.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}   outputTypes.clear();
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-					m->Groups.clear();
+					m->clearGroups();
 					delete input;
 					return 0;
 		}
@@ -524,11 +528,11 @@ int CollectSharedCommand::execute(){
 			delete cCurve;
 			
 			if (m->control_pressed) { 
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}  outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}  outputTypes.clear();
 				for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
 				delete order; 
 				delete input;
-				m->Groups.clear();
+				m->clearGroups();
 				return 0;
 			}
 
@@ -538,7 +542,7 @@ int CollectSharedCommand::execute(){
 		for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}	
 		
 		//reset groups parameter
-		m->Groups.clear(); 
+		m->clearGroups(); 
 		delete input;
 		
 		m->mothurOutEndLine();