X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.cpp;h=0e0be0e8cf2799527e2664bb79b1cdded09e215c;hb=87537e4ee46cae9b7041ae0ed4dbbc229936d37c;hp=b627a6bda6e3fa63de073a4b3f6c20bee7a2a680;hpb=9354b70bb84f6dd52ff4a1955754bcbf7edeedbf;p=mothur.git

diff --git a/groupmap.cpp b/groupmap.cpp
index b627a6b..0e0be0e 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -12,8 +12,9 @@
 /************************************************************/
 
  GroupMap::GroupMap(string filename) {
+	m = MothurOut::getInstance();
 	groupFileName = filename;
-	openInputFile(filename, fileHandle);
+	m->openInputFile(filename, fileHandle);
 	index = 0;
 }
 
@@ -21,21 +22,29 @@
  GroupMap::~GroupMap(){}
 
 /************************************************************/
-void GroupMap::readMap() {
+int GroupMap::readMap() {
 		string seqName, seqGroup;
-	
+		int error = 0;
+
 		while(fileHandle){
-			fileHandle >> seqName;			//read from first column
+			fileHandle >> seqName;	m->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
-			seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
-		
-			gobble(fileHandle);
+			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
+			}
+			m->gobble(fileHandle);
 		}
 		fileHandle.close();
+		return error;
 }
 /************************************************************/
 int GroupMap::getNumGroups() { return namesOfGroups.size();	}
@@ -52,26 +61,28 @@ string GroupMap::getGroup(string sequenceName) {
 }
 
 /************************************************************/
+
 void GroupMap::setGroup(string sequenceName, string groupN) {
 	groupmap[sequenceName] = groupN;
 }
+
 /************************************************************/
 void GroupMap::setNamesOfGroups(string seqGroup) {
-			int i, count;
-			count = 0;
-			for (i=0; i<namesOfGroups.size(); i++) {
-				if (namesOfGroups[i] != seqGroup) {
-					count++; //you have not found this group
-				}else {
-					break; //you already have it
-				}
-			}
-			if (count == namesOfGroups.size()) {
-				namesOfGroups.push_back(seqGroup); //new group
-				seqsPerGroup[seqGroup] = 0;
-				groupIndex[seqGroup] = index;
-				index++;
-			}
+	int i, count;
+	count = 0;
+	for (i=0; i<namesOfGroups.size(); i++) {
+		if (namesOfGroups[i] != seqGroup) {
+			count++; //you have not found this group
+		}else {
+			break; //you already have it
+		}
+	}
+	if (count == namesOfGroups.size()) {
+		namesOfGroups.push_back(seqGroup); //new group
+		seqsPerGroup[seqGroup] = 0;
+		groupIndex[seqGroup] = index;
+		index++;
+	}
 }
 /************************************************************/
 bool GroupMap::isValidGroup(string groupname) {
@@ -83,7 +94,7 @@ bool GroupMap::isValidGroup(string groupname) {
 		return false;
 	}
 	catch(exception& e) {
-		errorOut(e, "GroupMap", "isValidGroup");
+		m->errorOut(e, "GroupMap", "isValidGroup");
 		exit(1);
 	}
 }
@@ -101,7 +112,7 @@ int GroupMap::getNumSeqs(string group) {
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "GroupMap", "getNumSeqs");
+		m->errorOut(e, "GroupMap", "getNumSeqs");
 		exit(1);
 	}
 }
@@ -119,7 +130,7 @@ vector<string> GroupMap::getNamesSeqs(){
 		return names;
 	}
 	catch(exception& e) {
-		errorOut(e, "GroupMap", "getNamesSeqs");
+		m->errorOut(e, "GroupMap", "getNamesSeqs");
 		exit(1);
 	}
 }