LibShuffCommand::LibShuffCommand(){
try {
- //globaldata = GlobalData::getInstance();
+ globaldata = GlobalData::getInstance();
+ convert(globaldata->getCutOff(), cutOff);
+ convert(globaldata->getIters(), iters);
+ matrix = globaldata->gMatrix;
+ coverageFile = getRootName(globaldata->getPhylipFile()) + "coverage";
+ summaryFile = getRootName(globaldata->getPhylipFile()) + "slsummary";
+ openOutputFile(coverageFile, out);
+ openOutputFile(summaryFile, outSum);
+
+ //set the groups to be analyzed
+ setGroups();
+
+ //file headers for coverage file
+ out << "D" << '\t';
+ for (int i = 0; i < groupComb.size(); i++) {
+ out << "C" + groupComb[i] << '\t';
+ }
+
+ for (int i = 0; i < numGroups; i++) {
+ for (int j = 0; j < numGroups; j++) {
+ //don't output AA to AA
+ if (i != j) {
+ out << "Delta" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
+ }
+ }
+ }
+ out << endl;
+
+ numComp = numGroups*numGroups;
+
+ coverage = new Coverage();
}
catch(exception& e) {
//**********************************************************************************************************************
LibShuffCommand::~LibShuffCommand(){
-
+ delete coverage;
}
//**********************************************************************************************************************
int LibShuffCommand::execute(){
try {
+ //deltaValues[0] = scores for the difference between AA and AB.
+ //cValues[0][0] = AA, cValues[0][1] = AB, cValues[0][2] = AC, cValues[1][0] = BA, cValues[1][1] = BB...
+
+ sumDelta.resize(numComp-numGroups, 0.0);
+
+ float D = 0.0;
+
+ /*****************************/
+ //get values for users matrix
+ /*****************************/
+ matrix->getMinsForRowsVectors();
+
+ //get values for users matrix
+ while (D <= cutOff) {
+ cValues = coverage->getValues(matrix, D);
+
+ //find delta values
+ int count = 0;
+ for (int i = 0; i < numGroups; i++) {
+ for (int j = 0; j < numGroups; j++) {
+ //don't save AA to AA
+ if (i != j) {
+ //(Caa - Cab)^2
+ deltaValues.push_back( (abs(cValues[i][i]-cValues[i][j]) * abs(cValues[i][i]-cValues[i][j])) );
+ sumDelta[count] += deltaValues[count];
+ count++;
+ }
+ }
+ }
+
+ D += 0.01;
+
+ printCoverageFile(D);
+
+ //clear out old Values
+ cValues.clear();
+ deltaValues.clear();
+ }
+
+ /*******************************************************************************/
+ //create and score random matrixes finding the sumDelta values for summary file
+ /******************************************************************************/
+
+ //initialize rsumDelta
+ rsumDelta.resize(numComp-numGroups);
+ for (int l = 0; l < rsumDelta.size(); l++) {
+ for (int w = 0; w < iters; w++) {
+ rsumDelta[l].push_back(0.0);
+ }
+ }
+
+ for (int m = 0; m < iters; m++) {
+ //generate random matrix in getValues
+ //values for random matrix
+ while (D <= cutOff) {
+ cValues = coverage->getValues(matrix, D);
+
+ //find delta values
+ int count = 0;
+ for (int i = 0; i < numGroups; i++) {
+ for (int j = 0; j < numGroups; j++) {
+ //don't save AA to AA
+ if (i != j) {
+ //(Caa - Cab)^2
+ rsumDelta[count][m] += (abs(cValues[i][i]-cValues[i][j]) * abs(cValues[i][i]-cValues[i][j]));
+ count++;
+ }
+ }
+ }
+
+ D += 0.01;
+
+ //clear out old Values
+ cValues.clear();
+ }
+ }
+
+ /**********************************************************/
+ //find the signifigance of the user matrix' sumdelta values
+ /**********************************************************/
+
+ for (int t = 0; t < rsumDelta.size(); t++) {
+ //sort rsumDelta t
+ sort(rsumDelta[t].begin(), rsumDelta[t].end());
+
+ //the index of the score higher than yours is returned
+ //so if you have 1000 random matrices the index returned is 100
+ //then there are 900 matrices with a score greater then you.
+ //giving you a signifigance of 0.900
+ int index = findIndex(sumDelta[t], t);
+
+ //the signifigance is the number of trees with the users score or higher
+ sumDeltaSig.push_back((iters-index)/(float)iters);
+
+ }
+
+ printSummaryFile();
+
+ //clear out users groups
+ globaldata->Groups.clear();
+
return 0;
}
catch(exception& e) {
exit(1);
}
}
+//**********************************************************************************************************************
+void LibShuffCommand::printCoverageFile(float d) {
+ try {
+ //format output
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ out << setprecision(globaldata->getIters().length()) << d << '\t';
+
+ //print out coverage values
+ for (int i = 0; i < numGroups; i++) {
+ for (int j = 0; j < numGroups; j++) {
+ out << cValues[i][j] << '\t';
+ }
+ }
+
+ //print out delta values
+ for (int i = 0; i < deltaValues.size(); i++) {
+ out << deltaValues[i] << '\t';
+ }
+
+ out << endl;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the LibShuffCommand class function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void LibShuffCommand::printSummaryFile() {
+ try {
+ //format output
+ outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
+
+ for (int i = 0; i < numGroups; i++) {
+ for (int j = 0; j < numGroups; j++) {
+ //don't output AA to AA
+ if (i != j) {
+ outSum << "Delta" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
+ }
+ }
+ }
+ outSum << endl;
+
+ //print out delta values
+ for (int i = 0; i < sumDelta.size(); i++) {
+ outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
+ }
+
+ outSum << endl;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the LibShuffCommand class function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
//**********************************************************************************************************************
+void LibShuffCommand::setGroups() {
+ try {
+ //if the user has not entered specific groups to analyze then do them all
+ if (globaldata->Groups.size() == 0) {
+ numGroups = globaldata->gGroupmap->getNumGroups();
+ for (int i=0; i < numGroups; i++) {
+ globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+ }
+ }else {
+ if (globaldata->getGroups() != "all") {
+ //check that groups are valid
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
+ cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
+ // erase the invalid group from globaldata->Groups
+ globaldata->Groups.erase (globaldata->Groups.begin()+i);
+ }
+ }
+
+ //if the user only entered invalid groups
+ if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
+ numGroups = globaldata->gGroupmap->getNumGroups();
+ for (int i=0; i < numGroups; i++) {
+ globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+ }
+ cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
+ }else { numGroups = globaldata->Groups.size(); }
+ }else { //users wants all groups
+ numGroups = globaldata->gGroupmap->getNumGroups();
+ globaldata->Groups.clear();
+ for (int i=0; i < numGroups; i++) {
+ globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+ }
+ }
+ }
+
+ // number of comparisons i.e. with groups A,B,C = AA, AB, AC, BA, BB, BC...;
+ for (int i=0; i<numGroups; i++) {
+ for (int l = 0; l < numGroups; l++) {
+ //set group comparison labels
+ groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
+ }
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the LibShuffCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+int LibShuffCommand::findIndex(float score, int index) {
+ try{
+ for (int i = 0; i < rsumDelta[index].size(); i++) {
+ if (rsumDelta[index][i] >= score) { return i; }
+ }
+ return rsumDelta[index].size();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the LibShuffCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************/
+
projects / mothur.git / blobdiff