changes while testing

[mothur.git] / collectdisplay.h

diff --git a/collectdisplay.h b/collectdisplay.h
index 15cc5a75a1f32edac6d234ea934ceffdad608301..781cea1824dc77cb445819c94aed3173786baa94 100644 (file)
--- a/collectdisplay.h
+++ b/collectdisplay.h
@@ -30,8 +30,12 @@ public:
                //figure out what groups are being compared in getValues
                //because we randomizes the order we need to put the results in the correct column in the output file
                int group1Index, group2Index, pos;
-               group1Index = shared[0]->getGroupIndex();
-               group2Index = shared[1]->getGroupIndex();
+               
+               vector<string> mGroups = m->getGroups();
+               for (int i = 0; i < mGroups.size(); i++) {
+                       if (shared[0]->getGroup() == mGroups[i]) { group1Index = i; }
+                       if (shared[1]->getGroup() == mGroups[i]) { group2Index = i; }
+               }
                
                numGroupComb = 0;
                int n = 1;
@@ -46,7 +50,7 @@ public:
                        }
                        n++;
                }
-               
+                       
                if ((estimate->getMultiple() == true) && all) { 
                        numGroupComb++; 
                        groupData.resize((numGroupComb*data.size()), 0);
@@ -72,14 +76,20 @@ public:
                        output->output(numSeqs, groupData);     
                }
        };
-       
+                                                                       
        void init(string s)             {       output->initFile(s);    };
        void reset()                    {       output->resetFile();    };
        void close()                    {       output->resetFile();    };
        void setAll(bool a)             {       all = a;                                }
        bool getAll()                   {       return all;                             }
        
-       bool isCalcMultiple() { return estimate->getMultiple(); }
+       
+       bool isCalcMultiple()   { return estimate->getMultiple(); }
+       bool calcNeedsAll()     { return estimate->getNeedsAll(); }
+       bool hasLciHci()        {
+               if (estimate->getCols() == 3) { return true; } 
+               else{ return false; } 
+       }
        
        string getName()        {  return estimate->getName();  }