X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.cpp;h=d57646e3e3dad937d3ca0fa81b26f402cfa1ad4d;hb=a8367302932de9be5434e77f6e5829d7609e2aec;hp=27302dbce43f02a008fa54aaeb5e84bda8a8b003;hpb=44c1323a88b2a697c7047df1b3bb8c59eadd15b1;p=mothur.git

diff --git a/groupmap.cpp b/groupmap.cpp
index 27302db..d57646e 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -12,37 +12,42 @@
 /************************************************************/
 
  GroupMap::GroupMap(string filename) {
+	m = MothurOut::getInstance();
 	groupFileName = filename;
 	openInputFile(filename, fileHandle);
 	index = 0;
 }
 
 /************************************************************/
- GroupMap::~GroupMap(){};
+ GroupMap::~GroupMap(){}
 
 /************************************************************/
-void GroupMap::readMap() {
+int GroupMap::readMap() {
 		string seqName, seqGroup;
-	
+		int error = 0;
+
 		while(fileHandle){
-			fileHandle >> seqName;			//read from first column
+			fileHandle >> seqName;	gobble(fileHandle);		//read from first column
 			fileHandle >> seqGroup;			//read from second column
 			
+			if (m->control_pressed) {  fileHandle.close();  return 1; }
+	
 			setNamesOfGroups(seqGroup);
-						
-			groupmap[seqName] = seqGroup;	//store data in map
-		
+			
+			it = groupmap.find(seqName);
+			
+			if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
+			else {
+				groupmap[seqName] = seqGroup;	//store data in map
+				seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
+			}
 			gobble(fileHandle);
 		}
 		fileHandle.close();
+		return error;
 }
 /************************************************************/
-
-int GroupMap::getNumGroups() {
-			
-	return namesOfGroups.size();	
-		
-}
+int GroupMap::getNumGroups() { return namesOfGroups.size();	}
 /************************************************************/
 
 string GroupMap::getGroup(string sequenceName) {
@@ -53,11 +58,13 @@ string GroupMap::getGroup(string sequenceName) {
 	}else {
 		return "not found";
 	}
-		
 }
 
 /************************************************************/
-
+void GroupMap::setGroup(string sequenceName, string groupN) {
+	groupmap[sequenceName] = groupN;
+}
+/************************************************************/
 void GroupMap::setNamesOfGroups(string seqGroup) {
 			int i, count;
 			count = 0;
@@ -70,7 +77,60 @@ void GroupMap::setNamesOfGroups(string seqGroup) {
 			}
 			if (count == namesOfGroups.size()) {
 				namesOfGroups.push_back(seqGroup); //new group
+				seqsPerGroup[seqGroup] = 0;
 				groupIndex[seqGroup] = index;
 				index++;
 			}
 }
+/************************************************************/
+bool GroupMap::isValidGroup(string groupname) {
+	try {
+		for (int i = 0; i < namesOfGroups.size(); i++) {
+			if (groupname == namesOfGroups[i]) { return true; }
+		}
+		
+		return false;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "isValidGroup");
+		exit(1);
+	}
+}
+/************************************************************/
+int GroupMap::getNumSeqs(string group) {
+	try {
+		
+		map<string, int>::iterator itNum;
+		
+		itNum = seqsPerGroup.find(group);
+		
+		if (itNum == seqsPerGroup.end()) { return 0; }
+		
+		return seqsPerGroup[group];
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "getNumSeqs");
+		exit(1);
+	}
+}
+
+/************************************************************/
+vector<string> GroupMap::getNamesSeqs(){
+	try {
+	
+		vector<string> names;
+		
+		for (it = groupmap.begin(); it != groupmap.end(); it++) {
+			names.push_back(it->first);
+		}
+		
+		return names;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "getNamesSeqs");
+		exit(1);
+	}
+}
+/************************************************************/
+