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

[mothur.git] / sharedlistvector.cpp

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 49780314bca4d40be6a96a9593831b39317faaca..f2d8e07f81320d58b500287dc66df8e068246ee5 100644 (file)
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -283,21 +283,42 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
                //fill vectors
                for(int i=0;i<numBins;i++){
                        names = get(i);  
-                       while (names.find_first_of(',') != -1) { 
-                               name = names.substr(0,names.find_first_of(','));
-                               names = names.substr(names.find_first_of(',')+1, names.length());
-                               group = groupmap->getGroup(name);
-                               if(group == "not found") {      m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
-                               finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+                       int nameLength = names.size();
+                       string seqName = "";
+                       
+                       for(int j=0;j<nameLength;j++){
+                               if(names[j] == ','){
+                                       group = groupmap->getGroup(seqName);
+                                       if(group == "not found") {      m->mothurOut("Error: Sequence '" + seqName + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+                                       finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+                                       
+                                       seqName = "";
+                               }
+                               else{
+                                       seqName += names[j];
+                               }
                        }
+                       group = groupmap->getGroup(seqName);
+                       if(group == "not found") {      m->mothurOut("Error: Sequence '" + seqName + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+                       finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+                       
+                       
+                       
+//                     while (names.find_first_of(',') != -1) { 
+//                             name = names.substr(0,names.find_first_of(','));
+//                             names = names.substr(names.find_first_of(',')+1, names.length());
+//                             group = groupmap->getGroup(name);
+//                             if(group == "not found") {      m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+//                             finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+//                     }
                        
                        //get last name
-                       group = groupmap->getGroup(names);
-                       if(group == "not found") {      m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
-                       finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+//                     group = groupmap->getGroup(names);
+//                     if(group == "not found") {      m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+//                     finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
                        
                }
-               
+
                return lookup;
        }
        catch(exception& e) {