X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=coverage.cpp;h=aebe66f1e0814f7a41fb9694403f87919fbcc660;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=6b514fbc2e47a40c8312ecfa206bc4d9e04a1e50;hpb=81ff02ef4064fe4dec986ea3110c1cb8e1285fe6;p=mothur.git

diff --git a/coverage.cpp b/coverage.cpp
index 6b514fb..aebe66f 100644
--- a/coverage.cpp
+++ b/coverage.cpp
@@ -2,107 +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.
  *
  */
 
-/* This class library coverage at the given distances of the Cramer-von Mises statistic.
-	you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries" 
-	paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0  
-	DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
-	
-	
 #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
+
+/***********************************************************************/