#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, float d, vector< vector<float> >& data) {
+ try {
+ vector<float> min;
+ vector<string> groups;
//initialize data
- data.resize(numGroups);
+ data.resize(numUserGroups);
for (int l = 0; l < data.size(); l++) {
data[l].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)) {
+
+ 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());
+//cout << "minvector for : " << globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[j] << endl;
+//for(int h = 0; h<min.size(); h++) {
+// cout << min[h] << " ";
+//}
+//cout << endl;
+ int index = -1;
+ //find index in min where value is higher than d
+ for (int m = 0; m < min.size(); m++) {
+ if (min[m] > d) { 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[a][b] = 1.0 - ((min.size()-index)/(float)min.size());
+//cout << "D = " << d << "data " << a << b << " = " << data[a][b] << endl;
+ if (b < numUserGroups-1) { b++; }
+ else{ //you are moving to a new row of "boxes"
+ b = 0;
+ a++;
+ }
+ }
+ count++;
+ }
+ }
+ }
+ 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";
+ 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);
+ }
+}
+//**********************************************************************************************************************
+//For the random matrices
+void Coverage::getValues(FullMatrix* matrix, float d, vector< vector<float> >& data, string r) {
+ try {
+ vector<float> min;
+ vector<string> groups;
+
+ //initialize data
+ data.resize(numUserGroups);
+ for (int l = 0; l < data.size(); l++) {
+ data[l].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)) {
+cout << "combo " << a << b << endl;
+cout << "original matrix mins4rows " << endl;
+matrix->printMinsForRows(cout);
+ //create random matrix for this comparison
+ matrix->shuffle(count);
+
+ min = matrix->getMins(count); //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
+cout << "shuffled matrix mins4rows " << endl;
+matrix->printMinsForRows(cout);
+
+ //find the coverage at this distance
+ sort(min.begin(), min.end());
+
+ int index = -1;
+ //find index in min where value is higher than d
+ for (int m = 0; m < min.size(); m++) {
+ if (min[m] > d) { 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[a][b] = 1.0 - ((min.size()-index)/(float)min.size());
+cout << "D = " << d << "data " << a << b << " = " << data[a][b] << endl;
+ if (b < numUserGroups-1) { b++; }
+ else{ //you are moving to a new row of "boxes"
+ b = 0;
+ a++;
+ }
+ }
+ count++;
+
+ //restore matrix to original form for next shuffle
+ matrix->restore();
+min = matrix->getMins(count-1);
+cout << "restored matrix mins4rows " << endl;
+matrix->printMinsForRows(cout);
+ }
+ }
}
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";
projects / mothur.git / blobdiff