changes to read.otu(list/shared) - took out substr calls

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index b627a6bda6e3fa63de073a4b3f6c20bee7a2a680..0e0be0e8cf2799527e2664bb79b1cdded09e215c 100644 (file)
--- 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);
        }
 }