added multiple processors option for Windows users to align.seqs, dist.seqs, summary...

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index 58e04c5db858791f28a99a5cb50795a570da0690..481fd1decfc4516eb5e1cf618c6b4d40cffbc8a9 100644 (file)
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -44,7 +44,7 @@ int GroupMap::readMap() {
                        m->gobble(fileHandle);
                }
                fileHandle.close();
-               m->namesOfGroups = namesOfGroups;
+               m->setAllGroups(namesOfGroups);
                return error;
 }
 /************************************************************/
@@ -70,7 +70,7 @@ int GroupMap::readDesignMap() {
                        m->gobble(fileHandle);
                }
                fileHandle.close();
-               m->namesOfGroups = namesOfGroups;
+               m->setAllGroups(namesOfGroups);
                return error;
 }
 
@@ -91,7 +91,15 @@ string GroupMap::getGroup(string sequenceName) {
 /************************************************************/
 
 void GroupMap::setGroup(string sequenceName, string groupN) {
-       groupmap[sequenceName] = groupN;
+       setNamesOfGroups(groupN);
+       
+       it = groupmap.find(sequenceName);
+       
+       if (it != groupmap.end()) {  m->mothurOut("Your groupfile contains more than 1 sequence named " + sequenceName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
+       else {
+               groupmap[sequenceName] = groupN;        //store data in map
+               seqsPerGroup[groupN]++;  //increment number of seqs in that group
+       }
 }
 
 /************************************************************/