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(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)) {
-
- 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) {
+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(numUserGroups);
+ 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);
+ }
}
/**************************************/
//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);
+
+ 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;
-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; }
- }
+ //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(); }
+ // 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;
+ //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();
+ }
}
- 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