moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / spearman.cpp

diff --git a/spearman.cpp b/spearman.cpp
deleted file mode 100644 (file)
index 49d5265..0000000
--- a/spearman.cpp
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- *  spearman.cpp
- *  Mothur
- *
- *  Created by westcott on 12/15/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "spearman.h"
-
-/***********************************************************************/
-
-EstOutput Spearman::getValues(vector<SharedRAbundVector*> shared) {
-       try {
-               data.resize(1,0);
-               
-               SAbundVector savA = shared[0]->getSAbundVector();
-               SAbundVector savB = shared[1]->getSAbundVector();
-               
-               double sumRanks = 0.0;
-               int numOTUS = shared[0]->getNumBins();
-               
-               vector<double> rankVectorA(savA.getMaxRank()+1, 0);
-               int currentRankA = 0;
-               for(int i=savA.getMaxRank();i>0;i--){   
-                       int numWithAbundanceI = savA.get(i);
-
-                       if(numWithAbundanceI > 1){      rankVectorA[i] = (currentRankA + 1 + currentRankA + numWithAbundanceI) / 2.0;   }
-                       else                                    {       rankVectorA[i] = currentRankA+numWithAbundanceI;        }
-                       currentRankA += numWithAbundanceI;
-               }
-               rankVectorA[0] = (numOTUS + currentRankA + 1) / 2.0;
-               
-               
-               vector<double> rankVectorB(savB.getMaxRank()+1, 0);
-               int currentRankB = 0;
-               for(int i=savB.getMaxRank();i>0;i--){   
-                       int numWithAbundanceI = savB.get(i);
-                       
-                       if(numWithAbundanceI > 1){      rankVectorB[i] = (currentRankB + 1 + currentRankB + numWithAbundanceI) / 2.0;   }
-                       else                                    {       rankVectorB[i] = currentRankB+numWithAbundanceI;        }
-                       currentRankB += numWithAbundanceI;
-               }
-               rankVectorB[0] = (numOTUS + currentRankB + 1) / 2.0;
-               
-               
-
-               for (int i = 0; i < shared[0]->getNumBins(); i++) { 
-                       int Aij = shared[0]->getAbundance(i);
-                       int Bij = shared[1]->getAbundance(i);
-                       
-                       float rankA = rankVectorA[Aij];
-                       float rankB = rankVectorB[Bij];
-                       
-                       sumRanks += ((rankA - rankB) * (rankA - rankB));
-               }
-               data[0] = 1.0 - ((6 * sumRanks) / (float) (numOTUS * ((numOTUS*numOTUS)-1)));
-               
-               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-               
-               return data;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Spearman", "getValues");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-