changes while testing

[mothur.git] / collectdisplay.h

diff --git a/collectdisplay.h b/collectdisplay.h
index af97c756d6a813959cabf5ce8f13f9e70f206806..781cea1824dc77cb445819c94aed3173786baa94 100644 (file)
--- a/collectdisplay.h
+++ b/collectdisplay.h
@@ -8,8 +8,6 @@
 #include "display.h"
 
 
-using namespace std;
-
 /***********************************************************************/
 
 class CollectDisplay : public Display {
@@ -17,21 +15,27 @@ class CollectDisplay : public Display {
 public:
        CollectDisplay(Calculator* calc, FileOutput* file) : estimate(calc), output(file) {timesCalled = 0;};
        ~CollectDisplay()       {       delete estimate; delete output;         }
+       
+       
        void update(SAbundVector* rank){
                nSeqs=rank->getNumSeqs();
                data = estimate->getValues(rank);
                output->output(nSeqs, data);    
        };
        
-       void update(SharedRAbundVector* shared1, SharedRAbundVector* shared2, int numSeqs, int numGroups){
+       void update(vector<SharedRAbundVector*> shared, int numSeqs, int numGroups){
                timesCalled++;
-               data = estimate->getValues(shared1, shared2);  //passes estimators a shared vector from each group to be compared
+               data = estimate->getValues(shared);  //passes estimators a shared vector from each group to be compared
                
                //figure out what groups are being compared in getValues
-               //because the jumble parameter randomizes the order we need to put the results in the correct column in the output file
+               //because we randomizes the order we need to put the results in the correct column in the output file
                int group1Index, group2Index, pos;
-               group1Index = shared1->getGroupIndex();
-               group2Index = shared2->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;
@@ -46,12 +50,25 @@ public:
                        }
                        n++;
                }
-
-               groupData.resize((numGroupComb*data.size()), 0);
-               
-               //fills groupdata with datas info
-               for (int i = 0; i < data.size(); i++) {
-                       groupData[pos+i] = data[i];
+                       
+               if ((estimate->getMultiple() == true) && all) { 
+                       numGroupComb++; 
+                       groupData.resize((numGroupComb*data.size()), 0);
+                       //is this the time its called with all values
+                       if  ((timesCalled % numGroupComb) == 0) { 
+                               //last spot
+                               pos = ((groupData.size()-1) * data.size());
+                       }
+                       //fills groupdata with datas info
+                       for (int i = 0; i < data.size(); i++) {
+                               groupData[pos+i] = data[i];
+                       }
+               }else {
+                       groupData.resize((numGroupComb*data.size()), 0);
+                       //fills groupdata with datas info
+                       for (int i = 0; i < data.size(); i++) {
+                               groupData[pos+i] = data[i];
+                       }
                }
                
                //when you get all your groups info then output
@@ -59,17 +76,33 @@ 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 calcNeedsAll()     { return estimate->getNeedsAll(); }
+       bool hasLciHci()        {
+               if (estimate->getCols() == 3) { return true; } 
+               else{ return false; } 
+       }
+       
+       string getName()        {  return estimate->getName();  }
+       
        
 private:
+       
        Calculator* estimate;
        FileOutput* output;
        int nSeqs, timesCalled, numGroupComb;
        vector<double> data;
        vector<double> groupData;
+       bool all;
+       
 };
 
 /***********************************************************************/