added list parameter to get.seqs and remove.seqs and added readline library for inter...

[mothur.git] / sharedlistvector.cpp

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 6cac9b1d9512a16d15eef553d351de0b16771b6e..4303cfde13d3c4250c8f952c7a6eeb4bd9a2553d 100644 (file)
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -263,10 +263,8 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
        try {
                SharedUtil* util;
                util = new SharedUtil();
-               vector<SharedRAbundVector*> lookup;
-               vector<SharedRAbundVector*> lookup2;
-               map<string, SharedRAbundVector*> finder;
-               map<string, SharedRAbundVector*>::iterator it;
+               vector<SharedRAbundVector*> lookup;  //contains just the groups the user selected
+               map<string, SharedRAbundVector*> finder;  //contains all groups in groupmap
                string group, names, name;
        
                util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
@@ -277,10 +275,11 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
                        finder[globaldata->gGroupmap->namesOfGroups[i]] = temp;
                        finder[globaldata->gGroupmap->namesOfGroups[i]]->setLabel(label);
                        finder[globaldata->gGroupmap->namesOfGroups[i]]->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
-                       //*temp = getSharedRAbundVector(globaldata->Groups[i]);
-                       lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]);
+                       if (inVector(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups)) {  //if this group is in user groups
+                               lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]);
+                       }
                }
-//cout << "after blanks" << endl;              
+       
                //fill vectors
                for(int i=0;i<numBins;i++){
                        names = get(i);  
@@ -288,30 +287,18 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
                                name = names.substr(0,names.find_first_of(','));
                                names = names.substr(names.find_first_of(',')+1, names.length());
                                group = groupmap->getGroup(name);
-//cout << i << '\t' << name << '\t' << group << endl;
                                if(group == "not found") {      mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); 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);
-//cout << i << '\t' << names << '\t' << group << endl;
                        if(group == "not found") {      mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine();  exit(1); }
                        finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
                        
                }
                
-               if (globaldata->Groups.size() == globaldata->gGroupmap->namesOfGroups.size()) { //no groups specified
-                       lookup2 = lookup;
-               }else{ //delete unwanted groups
-                       for (int i = 0; i < globaldata->Groups.size(); i++) {
-                               SharedRAbundVector* temp = new SharedRAbundVector(*finder[globaldata->Groups[i]]);
-                               lookup2.push_back(temp);
-                               delete finder[globaldata->Groups[i]];  //so we don't get dup memory
-                       }
-               }
-               
-               return lookup2;
+               return lookup;
        }
        catch(exception& e) {
                errorOut(e, "SharedListVector", "getSharedRAbundVector");