X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=coverage.cpp;h=6b514fbc2e47a40c8312ecfa206bc4d9e04a1e50;hb=81ff02ef4064fe4dec986ea3110c1cb8e1285fe6;hp=e7baf001fefe4d5de552c1cd6362eaa2b1333d2c;hpb=42b802c0006d8b13bd5b27ea48d032a85d3f2102;p=mothur.git

diff --git a/coverage.cpp b/coverage.cpp
index e7baf00..6b514fb 100644
--- a/coverage.cpp
+++ b/coverage.cpp
@@ -7,24 +7,92 @@
  *
  */
 
+/* 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"
 
 //**********************************************************************************************************************
-vector< vector<float> > Coverage::getValues(FullMatrix*, float) {
-	try {
+Coverage::Coverage() {
 		globaldata = GlobalData::getInstance();
-		numGroups = globaldata->Groups.size();
+		numUserGroups = globaldata->Groups.size();
+		numGroups = globaldata->gGroupmap->getNumGroups();
+}
+
+//**********************************************************************************************************************
+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(numGroups);
+		data.resize(dist.size());
 		for (int l = 0; l < data.size(); l++) {
-			data[l].push_back(0.0);
+			data[l].resize(numGroups);
+			for (int k = 0; k < data[l].size(); k++) {
+				data[l][k].push_back(0.0);
+			}
 		}
 
 		/**************************************/
-		//get the minumums for each comparision
+		//get the minimums for each comparision
 		/**************************************/
-		return data;
+		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;
+
+					//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();
+					}
+				}
+			}
+		}
+		
 	}
 	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";