X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removeotuscommand.cpp;h=16fd8dce8bab96b030a57effd81d218e122628a5;hp=0fbed18b8be943fc4134cc18555c5a25cbd25b74;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 0fbed18..16fd8dc 100644
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -14,13 +14,13 @@
 //**********************************************************************************************************************
 vector<string> RemoveOtusCommand::setParameters(){	
 	try {
-		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
-		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-		CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
-		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-		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 pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pgroup);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(plist);
+		CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+		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);		}
@@ -52,7 +52,22 @@ string RemoveOtusCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string RemoveOtusCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "group")       {   pattern = "[filename],[tag],pick,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],[tag],pick,[extension]";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "RemoveOtusCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 ///**********************************************************************************************************************
 RemoveOtusCommand::RemoveOtusCommand(){	
 	try {
@@ -182,12 +197,13 @@ 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; }
@@ -195,7 +211,7 @@ 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();
@@ -229,14 +245,20 @@ 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);
+		map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[tag]"] = label;
+        variables["[extension]"] = m->getExtension(listfile);
+		string outputFileName = getOutputFileName("list", variables);
 		
 		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);
+		variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+        variables["[extension]"] = m->getExtension(groupfile);
+		string outputGroupFileName = getOutputFileName("group", variables);
 		
 		ofstream outGroup;
 		m->openOutputFile(outputGroupFileName, outGroup);
@@ -258,7 +280,7 @@ 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);
@@ -292,7 +314,7 @@ 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;
@@ -406,30 +428,6 @@ 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);
-	}
-}
-//**********************************************************************************************************************