added groups option to get.oturep command

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index b627a6bda6e3fa63de073a4b3f6c20bee7a2a680..d57646e3e3dad937d3ca0fa81b26f402cfa1ad4d 100644 (file)
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -12,6 +12,7 @@
 /************************************************************/
 
  GroupMap::GroupMap(string filename) {
+       m = MothurOut::getInstance();
        groupFileName = filename;
        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;  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
-               
+                       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();    }
@@ -83,7 +92,7 @@ bool GroupMap::isValidGroup(string groupname) {
                return false;
        }
        catch(exception& e) {
-               errorOut(e, "GroupMap", "isValidGroup");
+               m->errorOut(e, "GroupMap", "isValidGroup");
                exit(1);
        }
 }
@@ -101,7 +110,7 @@ int GroupMap::getNumSeqs(string group) {
                
        }
        catch(exception& e) {
-               errorOut(e, "GroupMap", "getNumSeqs");
+               m->errorOut(e, "GroupMap", "getNumSeqs");
                exit(1);
        }
 }
@@ -119,7 +128,7 @@ vector<string> GroupMap::getNamesSeqs(){
                return names;
        }
        catch(exception& e) {
-               errorOut(e, "GroupMap", "getNamesSeqs");
+               m->errorOut(e, "GroupMap", "getNamesSeqs");
                exit(1);
        }
 }