X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeotuscommand.cpp;h=54adeb244693bb13e22884248e71deadeb5e2144;hb=ce8794490ab1d83adcdb2b92e0302a1e43e17adf;hp=30f337bf7fffc90bcdf7d9ebb8cc97611c6ebd29;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 30f337b..54adeb2 100644
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -52,7 +52,27 @@ string RemoveOtusCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string RemoveOtusCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "group")            {   outputFileName = "pick" + m->getExtension(inputName);  }
+            else if (type == "list")        {   outputFileName = "pick" + m->getExtension(inputName);  }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RemoveOtusCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 ///**********************************************************************************************************************
 RemoveOtusCommand::RemoveOtusCommand(){	
 	try {
@@ -134,7 +154,8 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
 			//check for required parameters
 			accnosfile = validParameter.validFile(parameters, "accnos", true);
 			if (accnosfile == "not open") { abort = true; }
-			else if (accnosfile == "not found") {  accnosfile = ""; }	
+			else if (accnosfile == "not found") {  accnosfile = ""; }
+			else { m->setAccnosFile(accnosfile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }
@@ -142,7 +163,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
 				groupfile = m->getGroupFile(); 
 				if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setGroupFile(groupfile); }	
 			
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { abort = true; }
@@ -150,7 +171,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
 				listfile = m->getListFile(); 
 				if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setListFile(listfile); }	
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }
@@ -181,12 +202,13 @@ int RemoveOtusCommand::execute(){
 		groupMap->readMap();
 		
 		//get groups you want to remove
-		if (accnosfile != "") { readAccnos(); }
+		if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups);  }
 		
 		//make sure groups are valid
 		//takes care of user setting groupNames that are invalid or setting groups=all
 		SharedUtil* util = new SharedUtil();
-		util->setGroups(Groups, groupMap->namesOfGroups);
+		vector<string> allGroups = groupMap->getNamesOfGroups();
+		util->setGroups(Groups, allGroups);
 		delete util;
 		
 		if (m->control_pressed) { delete groupMap; return 0; }
@@ -194,7 +216,7 @@ int RemoveOtusCommand::execute(){
 		//read through the list file keeping any otus that contain any sequence from the groups selected
 		readListGroup();
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 		
 		if (outputNames.size() != 0) {
 			m->mothurOutEndLine();
@@ -228,14 +250,14 @@ int RemoveOtusCommand::readListGroup(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick." + label +  m->getExtension(listfile);
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("list", listfile);
 		
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
 		string GroupOutputDir = outputDir;
 		if (outputDir == "") {  GroupOutputDir += m->hasPath(groupfile);  }
-		string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick." + label  + m->getExtension(groupfile);
+		string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + label + "." + getOutputFileNameTag("group", groupfile);
 		
 		ofstream outGroup;
 		m->openOutputFile(outputGroupFileName, outGroup);
@@ -257,7 +279,7 @@ int RemoveOtusCommand::readListGroup(){
 		//as long as you are not at the end of the file or done wih the lines you want
 		while((list != NULL) && (userLabels.size() != 0)) {
 			
-			if (m->control_pressed) {  delete list; delete input; out.close();  outGroup.close(); remove(outputFileName.c_str());  remove(outputGroupFileName.c_str());return 0;  }
+			if (m->control_pressed) {  delete list; delete input; out.close();  outGroup.close(); m->mothurRemove(outputFileName);  m->mothurRemove(outputGroupFileName);return 0;  }
 			
 			if(labels.count(list->getLabel()) == 1){
 				processList(list, groupMap, out, outGroup, wroteSomething);
@@ -291,7 +313,7 @@ int RemoveOtusCommand::readListGroup(){
 		}
 		
 		
-		if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); remove(outputFileName.c_str());  remove(outputGroupFileName.c_str()); return 0;  }
+		if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName);  m->mothurRemove(outputGroupFileName); return 0;  }
 		
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
@@ -405,30 +427,6 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr
 	}
 }
 //**********************************************************************************************************************
-void RemoveOtusCommand::readAccnos(){
-	try {
-		Groups.clear();
-		
-		ifstream in;
-		m->openInputFile(accnosfile, in);
-		string name;
-		
-		while(!in.eof()){
-			in >> name;
-			
-			Groups.push_back(name);
-			
-			m->gobble(in);
-		}
-		in.close();		
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "RemoveOtusCommand", "readAccnos");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************