* 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
+
+/***********************************************************************/
projects / mothur.git / blobdiff