changes while testing

[mothur.git] / coverage.cpp

diff --git a/coverage.cpp b/coverage.cpp
index cd8138d7dd6216e31f0617a45cb7b0bd63d5dbb5..aebe66f1e0814f7a41fb9694403f87919fbcc660 100644 (file)
--- a/coverage.cpp
+++ b/coverage.cpp
@@ -2,101 +2,28 @@
  *  coverage.cpp
  *  Mothur
  *
- *  Created by Sarah Westcott on 3/9/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *  Created by Pat Schloss on 4/22/09.
+ *  Copyright 2009 Patrick D. Schloss. All rights reserved.
  *
  */
 
 #include "coverage.h"
 
-//**********************************************************************************************************************
-Coverage::Coverage() {
-               globaldata = GlobalData::getInstance();
-               numUserGroups = globaldata->Groups.size();
-               numGroups = globaldata->gGroupmap->getNumGroups();
-}
+/***********************************************************************/
+EstOutput Coverage::getValues(SAbundVector* rank){
 
-//**********************************************************************************************************************
-void Coverage::getValues(FullMatrix* matrix, vector< vector< vector<float> > >& data, vector<float> dist, string mode) {
        try {
-               vector<float> min;
-               vector<string> groups;
-               
-               //initialize data
-               data.resize(dist.size());
-               for (int l = 0; l < data.size(); l++) {
-                       data[l].resize(numGroups);
-                       for (int k = 0; k < data[l].size(); k++) {
-                               data[l][k].push_back(0.0);
-                       }
-               }
-
-               /**************************************/
-               //get the minimums for each comparision
-               /**************************************/
-               int count = 0;
-               int a = 0;
-               int b = 0;
-               for (int i = 0; i < numGroups; i++) {
-                       for (int j = 0; j < numGroups; j++) {
-                       
-                               //is this "box" one hte user wants analyzed?
-                               if ((inUsersGroups(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups) == true) && (inUsersGroups(globaldata->gGroupmap->namesOfGroups[j], globaldata->Groups) == true)) {
-                                       
-                                       if (mode == "random") {
-                                               //create random matrix for this comparison
-                                               matrix->shuffle(globaldata->gGroupmap->namesOfGroups[i], globaldata->gGroupmap->namesOfGroups[j]);
-                                       }
-                       
-                                       min = matrix->getMins(count);  //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
+               data.resize(1,0);
 
-                                       //find the coverage at this distance
-                                       sort(min.begin(), min.end());
-                                       
-                                       //loop through each distance and fill data
-                                       for (int k = 0; k < data.size(); k++) {
-                                       
-                                               int index = -1;
-                                               //find index in min where value is higher than d
-                                               for (int m = 0; m < min.size(); m++) {
-                                                       if (min[m] > dist[k])   { index = m; break;     }
-                                               }
-                                       
-                                               // if you don't find one than all the mins are less than d
-                                               if (index == -1) { index = min.size();  }
-                                       
-                                               //save value in data
-                                               data[k][a][b] = 1.0 - ((min.size()-index)/(float)min.size());
-       
-                                       }
-                                       
-                                       //move to next box
-                                       if (b < numUserGroups-1) {  b++;  }
-                                       else{ //you are moving to a new row of "boxes"
-                                               b = 0;
-                                               a++;
-                                       }
-
-                                       count++;
-                                       
-                                       if (mode == "random") {
-                                               //restore matrix to original form for next shuffle
-                                               matrix->restore();
-                                       }
-                               }
-                       }
-               }
+               data[0] = 1. - rank->get(1) / (double)rank->getNumSeqs();
                
+               return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "Coverage", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
-//**********************************************************************************************************************
 
-       
\ No newline at end of file
+
+/***********************************************************************/