Adds selectedGroups to sequenceParser class

#220

source/commands/chimeraperseuscommand.cpp

@@ -600,7 +600,8 @@ int ChimeraPerseusCommand::execute(){
             }else {
                 if (groupFile != "") {
                     //Parse sequences by group
-                    parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
+                    vector<string> temp;
+                    parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile, temp);
                     vector<string> groups = parser->getNamesOfGroups();
                     
                     if (m->control_pressed) { delete parser; for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  return 0; }

source/commands/chimeraslayercommand.cpp

@@ -1042,7 +1042,8 @@ int ChimeraSlayerCommand::setUpForSelfReference(SequenceParser*& parser, map<str
 			fileGroup[fastaFileNames[s]] = "noGroup";
 		}else {
 			//Parse sequences by group
-			parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
+            vector<string> temp;
+			parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile, temp);
 			vector<string> groups = parser->getNamesOfGroups();
 			
 			for (int i = 0; i < groups.size(); i++) {

source/commands/chimerauchimecommand.cpp

@@ -689,13 +689,13 @@ int ChimeraUchimeCommand::execute(){
 				//Parse sequences by group
                 vector<string> groups;
                 map<string, string> uniqueNames;
+                vector<string> temp;
                 if (hasCount) {
-                    vector<string> temp;
                     cparser = new SequenceCountParser(nameFile, fastaFileNames[s], temp);
                     groups = cparser->getNamesOfGroups();
                     uniqueNames = cparser->getAllSeqsMap();
                 }else{
-                    sparser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
+                    sparser = new SequenceParser(groupFile, fastaFileNames[s], nameFile, temp);
                     groups = sparser->getNamesOfGroups();
                     uniqueNames = sparser->getAllSeqsMap();
                 }

source/commands/chimeravsearchcommand.cpp

@@ -642,13 +642,13 @@ int ChimeraVsearchCommand::execute(){
                 //Parse sequences by group
                 vector<string> groups;
                 map<string, string> uniqueNames;
+                vector<string> temp;
                 if (hasCount) {
-                    vector<string> temp;
                     cparser = new SequenceCountParser(nameFile, fastaFileNames[s], temp);
                     groups = cparser->getNamesOfGroups();
                     uniqueNames = cparser->getAllSeqsMap();
                 }else{
-                    sparser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
+                    sparser = new SequenceParser(groupFile, fastaFileNames[s], nameFile, temp);
                     groups = sparser->getNamesOfGroups();
                     uniqueNames = sparser->getAllSeqsMap();
                 }

source/commands/preclustercommand.cpp

@@ -601,8 +601,8 @@ int PreClusterCommand::driverGroups(string newFFile, string newNFile, string new
         if (countfile != "") {
             cparser = new SequenceCountParser(countfile, fastafile, subsetGroups);
         }else {
-            if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile);	}
-            else				{ parser = new SequenceParser(groupfile, fastafile);			}
+            if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile, subsetGroups);	}
+            else				{ parser = new SequenceParser(groupfile, fastafile, subsetGroups);              }
         }
         
 		int numSeqs = 0;

source/commands/shhhseqscommand.cpp

@@ -213,7 +213,8 @@ int ShhhSeqsCommand::execute() {
 		
 		if (groupfile != "") {
 			//Parse sequences by group
-			SequenceParser parser(groupfile, fastafile, namefile);
+            vector<string> temp;
+			SequenceParser parser(groupfile, fastafile, namefile, temp);
 			vector<string> groups = parser.getNamesOfGroups();
 			
 			if (m->control_pressed) {  return 0; }

source/commands/splitgroupscommand.cpp

@@ -270,8 +270,8 @@ int SplitGroupCommand::execute(){
 int SplitGroupCommand::runNameGroup(){
 	try {
         SequenceParser* parser;
-		if (namefile == "") {	parser = new SequenceParser(groupfile, fastafile);				}
-		else				{	parser = new SequenceParser(groupfile, fastafile, namefile);	}
+		if (namefile == "") {	parser = new SequenceParser(groupfile, fastafile, Groups);				}
+		else				{	parser = new SequenceParser(groupfile, fastafile, namefile, Groups);	}
 		
 		if (m->control_pressed) { delete parser; return 0; }
         

source/datastructures/sequencecountparser.cpp

@@ -7,6 +7,7 @@
 //
 
 #include "sequencecountparser.h"
+#include "sharedutilities.h"
 
 /************************************************************/
 SequenceCountParser::SequenceCountParser(string countfile, string fastafile, vector<string> groupsSelected) {
@@ -24,6 +25,7 @@ SequenceCountParser::SequenceCountParser(string countfile, string fastafile, vec
             namesOfGroups = countTable.getNamesOfGroups();
             for (int i = 0; i < allNames.size(); i++) { indexes.push_back(i); }
         }else{
+            SharedUtil util;  util.setGroups(groupsSelected, namesOfGroups);
             namesOfGroups = groupsSelected;
             map<string, int> temp;
             for (int i = 0; i < allNames.size(); i++) {
@@ -67,6 +69,7 @@ SequenceCountParser::SequenceCountParser(string fastafile, CountTable& countTabl
                 namesOfGroups = countTable.getNamesOfGroups();
                 for (int i = 0; i < allNames.size(); i++) { indexes.push_back(i); }
             }else{
+                SharedUtil util;  util.setGroups(groupsSelected, namesOfGroups);
                 namesOfGroups = groupsSelected;
                 map<string, int> temp;
                 for (int i = 0; i < allNames.size(); i++) {