#include "libshuffcommand.h"
+#include "libshuff.h"
+#include "slibshuff.h"
+#include "dlibshuff.h"
//**********************************************************************************************************************
-
LibShuffCommand::LibShuffCommand(){
try {
- globaldata = GlobalData::getInstance();
- convert(globaldata->getCutOff(), cutOff);
- convert(globaldata->getIters(), iters);
- convert(globaldata->getStep(), step);
- form = globaldata->getForm();
- matrix = globaldata->gMatrix;
- coverageFile = getRootName(globaldata->getPhylipFile()) + "coverage";
- summaryFile = getRootName(globaldata->getPhylipFile()) + "slsummary";
- openOutputFile(coverageFile, out);
- openOutputFile(summaryFile, outSum);
+ srand( (unsigned)time( NULL ) );
- //set the groups to be analyzed
- setGroups();
+ globaldata = GlobalData::getInstance();
+ convert(globaldata->getCutOff(), cutOff); //get the cutoff
+ convert(globaldata->getIters(), iters); //get the number of iterations
+ convert(globaldata->getStep(), step); //get the step size for the discrete command
+ matrix = globaldata->gMatrix; //get the distance matrix
+ setGroups(); //set the groups to be analyzed
- //file headers for coverage file
- out << "D" << '\t';
- for (int i = 0; i < groupComb.size(); i++) {
- out << "C" + groupComb[i] << '\t';
+ if(globaldata->getForm() == "discrete"){
+ form = new DLibshuff(matrix, iters, step, cutOff);
}
-
- 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';
- }
- }
+ else{
+ form = new SLibshuff(matrix, iters, cutOff);
}
- out << endl;
-
- numComp = numGroups*numGroups;
-
- coverage = new Coverage();
-
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
//**********************************************************************************************************************
-LibShuffCommand::~LibShuffCommand(){
- delete coverage;
-}
-
-//**********************************************************************************************************************
-
int LibShuffCommand::execute(){
try {
- //deltaValues[0] = scores for the difference between AA and AB.
- //cValues[0][0][0] = AA at distance 0.0, cValues[0][0][1] = AB at distance 0.0, cValues[0][0][2] = AC at distance 0.0, cValues[0][1][0] = BA at distance 0.0, cValues[0][1][1] = BB...
- Progress* reading;
- reading = new Progress("Comparing to random:", iters);
-
- sumDelta.resize(numComp-numGroups, 0.0);
-
- matrix->setBounds();
-
- //load distances
- if (form != "discrete") { matrix->getDist(dist); }
- else {
- float f = 0.0;
- while (f <= cutOff) {
- dist.push_back(f);
- f += step;
- }
- }
-
- /*****************************/
- //get values for users matrix
- /*****************************/
-
- //clear out old Values
- deltaValues.clear();
- deltaValues.resize(dist.size());
-
- coverage->getValues(matrix, cValues, dist);
-
- float distDiff = 0;
-
- //loop through each distance and load sumdelta
- for (int p = 0; p < cValues.size(); p++) {
- //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 * distDiff
- deltaValues[p].push_back(((cValues[p][i][i]-cValues[p][i][j]) * (cValues[p][i][i]-cValues[p][i][j])) * distDiff); //* distDiff
- sumDelta[count] += deltaValues[p][count];
- count++;
- }
- }
- }
- if (p < cValues.size() - 1) {
- distDiff = dist[p+1] - dist[p];
- }
- }
-
- printCoverageFile();
-
- /*******************************************************************************/
- //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);
- }
- }
+ savedDXYValues = form->evaluateAll();
+ savedMinValues = form->getSavedMins();
+ pValueCounts.resize(numGroups);
+ for(int i=0;i<numGroups;i++){
+ pValueCounts[i].assign(numGroups, 0);
+ }
- for (int m = 0; m < iters; m++) {
- //generate random matrix in getValues
- //values for random matrix
+ Progress* reading = new Progress();
- coverage->getValues(matrix, cValues, dist, "random");
-
- //loop through each distance and load rsumdelta
- for (int p = 0; p < cValues.size(); p++) {
- //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) {
- //rsumDelta[3][500] = the sum of the delta scores for BB-BC for random matrix # 500.
- rsumDelta[count][m] += cValues[p][i][j]; // where cValues[p][0][1] = delta value at distance p of AA-AB, cValues[p][1][2] = delta value at distance p of BB-BC.
- count++;
- }
- }
+ for(int i=0;i<numGroups-1;i++) {
+ for(int j=i+1;j<numGroups;j++) {
+ reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
+ for(int p=0;p<iters;p++) {
+ form->randomizeGroups(i,j);
+ if(form->evaluatePair(i,j) >= savedDXYValues[i][j]) { pValueCounts[i][j]++; }
+ if(form->evaluatePair(j,i) >= savedDXYValues[j][i]) { pValueCounts[j][i]++; }
+ reading->update(p);
}
+ form->resetGroup(i);
+ form->resetGroup(j);
}
-
- //clear out old Values
- reading->update(m);
- cValues.clear();
-
}
-
reading->finish();
delete reading;
-
- /**********************************************************/
- //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);
- }
-
+ cout << endl;
printSummaryFile();
+ printCoverageFile();
//clear out users groups
globaldata->Groups.clear();
+ delete form;
return 0;
}
exit(1);
}
}
+
//**********************************************************************************************************************
+
void LibShuffCommand::printCoverageFile() {
try {
- //format output
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ ofstream outCov;
+ summaryFile = getRootName(globaldata->getPhylipFile()) + "libshuff.coverage";
+ openOutputFile(summaryFile, outCov);
+ outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
+ cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
+
+ map<double,vector<int> > allDistances;
+ map<double,vector<int> >::iterator it;
+
+ vector<vector<int> > indices(numGroups);
+ int numIndices = numGroups * numGroups;
- //loop through each distance
- for (int p = 0; p < cValues.size(); p++) {
- out << setprecision(6) << dist[p] << '\t';
- //print out coverage values
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- out << cValues[p][i][j] << '\t';
+ int index = 0;
+ for(int i=0;i<numGroups;i++){
+ indices[i].assign(numGroups,0);
+ for(int j=0;j<numGroups;j++){
+ indices[i][j] = index++;
+ for(int k=0;k<savedMinValues[i][j].size();k++){
+ if(allDistances[savedMinValues[i][j][k]].size() != 0){
+ allDistances[savedMinValues[i][j][k]][indices[i][j]]++;
+ }
+ else{
+ allDistances[savedMinValues[i][j][k]].assign(numIndices, 0);
+ allDistances[savedMinValues[i][j][k]][indices[i][j]] = 1;
+ }
}
}
-
- for (int h = 0; h < deltaValues[p].size(); h++) {
- out << deltaValues[p][h] << '\t';
+ }
+ it=allDistances.begin();
+
+ cout << setprecision(8);
+
+ vector<int> prevRow = it->second;
+ it++;
+
+ for(it;it!=allDistances.end();it++){
+ for(int i=0;i<it->second.size();i++){
+ it->second[i] += prevRow[i];
+ }
+ prevRow = it->second;
+ }
+
+ vector<int> lastRow = allDistances.rbegin()->second;
+ outCov << setprecision(8);
+
+ outCov << "dist";
+ for (int i = 0; i < numGroups; i++){
+ outCov << '\t' << groupNames[i];
+ }
+ for (int i=0;i<numGroups;i++){
+ for(int j=i+1;j<numGroups;j++){
+ outCov << '\t' << groupNames[i] << '-' << groupNames[j] << '\t';
+ outCov << groupNames[j] << '-' << groupNames[i];
}
-
- out << endl;
+ }
+ outCov << endl;
+
+ for(it=allDistances.begin();it!=allDistances.end();it++){
+ outCov << it->first << '\t';
+ for(int i=0;i<numGroups;i++){
+ outCov << it->second[indices[i][i]]/(float)lastRow[indices[i][i]] << '\t';
+ }
+ for(int i=0;i<numGroups;i++){
+ for(int j=i+1;j<numGroups;j++){
+ outCov << it->second[indices[i][j]]/(float)lastRow[indices[i][j]] << '\t';
+ outCov << it->second[indices[j][i]]/(float)lastRow[indices[j][i]] << '\t';
+ }
+ }
+ outCov << endl;
}
}
exit(1);
}
}
+
//**********************************************************************************************************************
+
void LibShuffCommand::printSummaryFile() {
try {
- //format output
+
+ ofstream outSum;
+ summaryFile = getRootName(globaldata->getPhylipFile()) + "libshuff.summary";
+ openOutputFile(summaryFile, outSum);
+
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
+ cout.setf(ios::fixed, ios::floatfield); cout.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';
- cout << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
+ cout << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
+ outSum << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
+
+ int precision = (int)log10(iters);
+ for(int i=0;i<numGroups;i++){
+ for(int j=i+1;j<numGroups;j++){
+ if(pValueCounts[i][j]){
+ cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
+ outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
+ }
+ else{
+ cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
+ outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
+ }
+ if(pValueCounts[j][i]){
+ cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
+ outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
+ }
+ else{
+ cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
+ outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
}
}
}
- outSum << endl;
- cout << endl;
- //print out delta values
- for (int i = 0; i < sumDelta.size(); i++) {
- if (sumDeltaSig[i] > (1/(float)iters)) {
- outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
- cout << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
- }else {
- outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << '\t';
- cout << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << '\t';
- }
- }
- outSum << endl;
- cout << 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";
}
//**********************************************************************************************************************
+
void LibShuffCommand::setGroups() {
try {
//if the user has not entered specific groups to analyze then do them all
for (int i=0; i < numGroups; i++) {
globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
}
- }else {
+ } else {
if (globaldata->getGroups() != "all") {
//check that groups are valid
for (int i = 0; i < globaldata->Groups.size(); 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
+ } else { numGroups = globaldata->Groups.size(); }
+ } else { //users wants all groups
numGroups = globaldata->gGroupmap->getNumGroups();
globaldata->Groups.clear();
for (int i=0; i < numGroups; i++) {
}
}
}
-
+
//sort so labels match
sort(globaldata->Groups.begin(), globaldata->Groups.end());
//sort
sort(globaldata->gGroupmap->namesOfGroups.begin(), globaldata->gGroupmap->namesOfGroups.end());
-
+ groupNames = globaldata->Groups;
+
// 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]);
- }
- }
+// 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);
}
}
-/***********************************************************/
-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