X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapsimcommand.cpp;h=e791f0c65c88e55b8eaf7a022c3d6be454633f69;hb=19fcbbdba99658f5eca244803280f9ee7f9f6607;hp=0ba5ef1f28261307e91d678a73b4993ff38fa0ec;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 0ba5ef1..e791f0c 100644
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -23,10 +23,10 @@
 //**********************************************************************************************************************
 vector<string> HeatMapSimCommand::setParameters(){	
 	try {
-		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);	
-		CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
+		CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);	
+		CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
 		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
-		CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);		
+		CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);		
 		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
 		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
 		CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
@@ -92,6 +92,7 @@ HeatMapSimCommand::HeatMapSimCommand(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 {
 			vector<string> myArray = setParameters();
@@ -157,21 +158,22 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
 			phylipfile = validParameter.validFile(parameters, "phylip", true);
 			if (phylipfile == "not open") { abort = true; }
 			else if (phylipfile == "not found") { phylipfile = ""; }	
-			else {  format = "phylip"; 	inputfile = phylipfile; if (outputDir == "") { outputDir += m->hasPath(phylipfile); }  }
+			else {  format = "phylip"; 	inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); }  }
 			
 			columnfile = validParameter.validFile(parameters, "column", true);
 			if (columnfile == "not open") { abort = true; }	
 			else if (columnfile == "not found") { columnfile = ""; }
-			else {  format = "column";	inputfile = columnfile; if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
+			else {  format = "column";	inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
 			if (sharedfile == "not open") { abort = true; }	
 			else if (sharedfile == "not found") { sharedfile = ""; }
-			else {  format = "shared";	inputfile = sharedfile;  if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
+			else {  format = "shared";	inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
 			
 			
 			//error checking on files			
@@ -222,6 +224,11 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
 				if (calc == "default")  {  calc = "jest-thetayc";  }
 			}
 			m->splitAtDash(calc, Estimators);
+			if (m->inUsersGroups("citation", Estimators)) { 
+				ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+				//remove citation from list of calcs
+				for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+			}
 				
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }
@@ -287,7 +294,7 @@ int HeatMapSimCommand::execute(){
 		
 		delete heatmap;
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear(); return 0; }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear(); return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -512,8 +519,8 @@ int HeatMapSimCommand::runCommandDist() {
 				map<string, int>::iterator itA = nameMap->find(first);
 				map<string, int>::iterator itB = nameMap->find(second);
 				
-				if(itA == nameMap->end()){  cerr << "AAError: Sequence '" << first << "' was not found in the names file, please correct\n"; exit(1);  }
-				if(itB == nameMap->end()){  cerr << "ABError: Sequence '" << second << "' was not found in the names file, please correct\n"; exit(1);  }
+				if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1);  }
+				if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1);  }
 				
 				//save distance
 				matrix[itA->second][itB->second] = dist;