X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapcommand.cpp;h=e07ae220eba02c86117feaa656e2b07015a4b94b;hp=cf5140a1c7a03db5603cd2358ea7797ea80701f6;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index cf5140a..e07ae22 100644
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -12,19 +12,19 @@
 //**********************************************************************************************************************
 vector<string> HeatMapCommand::setParameters(){	
 	try {
-		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
-		CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
-		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
-		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);	
-		CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
-		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-		CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "",false,false); parameters.push_back(pscale);
-		CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "",false,false); parameters.push_back(psorted);
-		CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "",false,false); parameters.push_back(pnumotu);
-		CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
+		CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prabund);
+		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(psabund);
+		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);	
+		CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prelabund);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+		CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "","",false,false); parameters.push_back(pscale);
+		CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "","",false,false); parameters.push_back(psorted);
+		CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnumotu);
+		CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		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);		}
@@ -61,6 +61,22 @@ string HeatMapCommand::getHelpString(){
 	}
 }
 
+//**********************************************************************************************************************
+string HeatMapCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "svg") {  pattern = "[filename],svg"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "HeatMapCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+
 //**********************************************************************************************************************
 HeatMapCommand::HeatMapCommand(){	
 	try {
@@ -151,29 +167,29 @@ HeatMapCommand::HeatMapCommand(string option) {
 			
 			//check for required parameters
 			listfile = validParameter.validFile(parameters, "list", true);
-			if (listfile == "not open") { listfile = ""; abort = true; }
+			if (listfile == "not open") { abort = true; }
 			else if (listfile == "not found") { listfile = ""; }
-			else {  format = "list"; inputfile = listfile; }
+			else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 			
 			sabundfile = validParameter.validFile(parameters, "sabund", true);
-			if (sabundfile == "not open") { sabundfile = ""; abort = true; }	
+			if (sabundfile == "not open") {  abort = true; }	
 			else if (sabundfile == "not found") { sabundfile = ""; }
-			else {  format = "sabund"; inputfile = sabundfile; }
+			else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 			
 			rabundfile = validParameter.validFile(parameters, "rabund", true);
-			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
+			if (rabundfile == "not open") {  abort = true; }	
 			else if (rabundfile == "not found") { rabundfile = ""; }
-			else {  format = "rabund"; inputfile = rabundfile; }
+			else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
-			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
+			if (sharedfile == "not open") { abort = true; }	
 			else if (sharedfile == "not found") { sharedfile = ""; }
-			else {  format = "sharedfile"; inputfile = sharedfile; }
+			else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 			
 			relabundfile = validParameter.validFile(parameters, "relabund", true);
-			if (relabundfile == "not open") { relabundfile = ""; abort = true; }	
+			if (relabundfile == "not open") {  abort = true; }	
 			else if (relabundfile == "not found") { relabundfile = ""; }
-			else {  format = "relabund"; inputfile = relabundfile; }
+			else {  format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
 			
 			
 			if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) { 
@@ -222,14 +238,14 @@ HeatMapCommand::HeatMapCommand(string option) {
 			if (groups == "not found") { groups = ""; }
 			else { 
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 			
 			string temp = validParameter.validFile(parameters, "numotu", false);		if (temp == "not found") { temp = "0"; }
-			convert(temp, numOTU);
+			m->mothurConvert(temp, numOTU);
 			
 			temp = validParameter.validFile(parameters, "fontsize", false);				if (temp == "not found") { temp = "24"; }
-			convert(temp, fontSize);
+			m->mothurConvert(temp, fontSize);
 			
 			sorted = validParameter.validFile(parameters, "sorted", false);				
 			if (sorted == "not found") { 
@@ -286,8 +302,8 @@ int HeatMapCommand::execute(){
 			while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 				if (m->control_pressed) {
 					for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
-					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
-					m->Groups.clear(); 
+					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+					m->clearGroups(); 
 					delete input; delete heatmap; return 0;
 				}
 		
@@ -329,8 +345,8 @@ int HeatMapCommand::execute(){
 			
 			
 			if (m->control_pressed) {
-				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
-				m->Groups.clear(); 
+				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+				m->clearGroups(); 
 				delete input; delete heatmap; return 0;
 			}
 
@@ -359,13 +375,13 @@ int HeatMapCommand::execute(){
 			}
 		
 			//reset groups parameter
-			m->Groups.clear();  
+			m->clearGroups();  
 			
 		}else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 	
 			while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 				if (m->control_pressed) {   
-					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 					delete rabund;  delete input; delete heatmap; return 0;	
 				}
 
@@ -404,7 +420,7 @@ int HeatMapCommand::execute(){
 			}
 			
 			if (m->control_pressed) {
-				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 				delete input; delete heatmap; return 0;
 			}
 
@@ -439,8 +455,8 @@ int HeatMapCommand::execute(){
 			while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 				if (m->control_pressed) {
 					for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
-					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
-					m->Groups.clear(); 
+					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+					m->clearGroups(); 
 					delete input; delete heatmap; return 0;
 				}
 		
@@ -481,8 +497,8 @@ int HeatMapCommand::execute(){
 			
 			
 			if (m->control_pressed) {
-				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
-				m->Groups.clear(); 
+				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+				m->clearGroups(); 
 				delete input; delete heatmap; return 0;
 			}
 
@@ -511,7 +527,7 @@ int HeatMapCommand::execute(){
 			}
 		
 			//reset groups parameter
-			m->Groups.clear();  
+			m->clearGroups();  
 
 		}
 		
@@ -519,7 +535,7 @@ int HeatMapCommand::execute(){
 		delete heatmap;
 		
 		if (m->control_pressed) {
-			for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear(); return 0;
+			for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear(); return 0;
 		}
 		
 		m->mothurOutEndLine();