* Dotur
*
* Created by Sarah Westcott on 11/18/08.
- * Copyright 2008 __MyCompanyName__. All rights reserved.
+ * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
void RareDisplay::init(string label){
try {
this->label = label;
- if(nIters != 1){
- openOutputFile(tempOutName, tempOutFile);
- openInputFile(tempInName, tempInFile);
- }
- else{
- openOutputFile(tempOutName, tempOutFile);
- }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function init. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the RareDisplay class function init. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "RareDisplay", "init");
exit(1);
}
}
int newNSeqs = rank->getNumSeqs();
vector<double> data = estimate->getValues(rank);
- if(nIters != 1){
-
- double oldNSeqs, oldMean, oldVar;
-
- tempInFile >> oldNSeqs >> oldMean >> oldVar;
-
- double oldS = oldVar * ( nIters - 2 );
- double delta = data[0] - oldMean;
- double newMean = oldMean + delta / nIters;
- double newS = oldS + delta * ( data[0] - newMean );
- double newVar = newS / ( nIters - 1 );
-
- tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
- }
- else{
- tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
- }
+ map<int, vector<double> >::iterator it = results.find(newNSeqs);
+ if (it == results.end()) { //first iter for this count
+ vector<double> temp;
+ temp.push_back(data[0]);
+ results[newNSeqs] = temp;
+ }else {
+ it->second.push_back(data[0]);
+ }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the RareDisplay class function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "RareDisplay", "update");
exit(1);
}
-};
+}
/***********************************************************************/
-void RareDisplay::update(SharedRAbundVector* shared1, SharedRAbundVector* shared2, int numSeqs, int numGroupComb) {
+void RareDisplay::update(vector<SharedRAbundVector*> shared, int numSeqs, int numGroupComb) {
try {
- vector<double> data = estimate->getValues(shared1, shared2);
- double newNSeqs = data[0];
-
- if(nIters != 1){
- double oldNSeqs, oldMean, oldVar;
-
- tempInFile >> oldNSeqs >> oldMean >> oldVar;
+ vector<double> data = estimate->getValues(shared);
- double oldS = oldVar * ( nIters - 2 );
- double delta = data[0] - oldMean;
- double newMean = oldMean + delta / nIters;
- double newS = oldS + delta * ( data[0] - newMean );
- double newVar = newS / ( nIters - 1 );
-
- tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
- }
- else{
- tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
- }
+ map<int, vector<double> >::iterator it = results.find(numSeqs);
+ if (it == results.end()) { //first iter for this count
+ vector<double> temp;
+ temp.push_back(data[0]);
+ results[numSeqs] = temp;
+ }else {
+ it->second.push_back(data[0]);
+ }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "RareDisplay", "update");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the RareDisplay class function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-};
+}
/***********************************************************************/
void RareDisplay::reset(){
try {
- if(nIters != 1){
- tempOutFile.close();
- tempInFile.close();
- }
- else{
- tempOutFile.close();
- }
-
nIters++;
-
- remove(tempInName.c_str());
- rename(tempOutName.c_str(), tempInName.c_str());
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function reset. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the RareDisplay class function reset. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "RareDisplay", "reset");
exit(1);
}
}
try {
output->initFile(label);
- openInputFile(tempInName, tempInFile);
-
- while(!tempInFile.eof()){
- int nSeqs;
- tempInFile >> nSeqs;
+ for (map<int, vector<double> >::iterator it = results.begin(); it != results.end(); it++) {
vector<double> data(3,0);
- double variance = 0;
+
+ sort((it->second).begin(), (it->second).end());
+
+ //lci=results[int(0.025*iter)] and hci=results[int(0.975*iter)]
+ data[0] = (it->second)[(int)(0.50*(nIters-1))];
+ //data[0] = m->getAverage(it->second);
+ data[1] = (it->second)[(int)(0.025*(nIters-1))];
+ data[2] = (it->second)[(int)(0.975*(nIters-1))];
+ //cout << nIters << '\t' << (int)(0.025*(nIters-1)) << '\t' << (int)(0.975*(nIters-1)) << endl;
+
+ //cout << it->first << '\t' << data[1] << '\t' << data[2] << endl;
- tempInFile >> data[0];
- tempInFile >> variance;
+ output->output(it->first, data);
+ }
- double ci = 1.96 * pow(variance, 0.5);
- data[1] = data[0] - ci;
- data[2] = data[0] + ci;
+ nIters = 1;
+ results.clear();
+
+ output->resetFile();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareDisplay", "close");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+void RareDisplay::inputTempFiles(string filename){
+ try {
+ ifstream in;
+ m->openInputFile(filename, in);
- output->output(nSeqs, data);
+ int thisIters, size;
+ in >> thisIters >> size; m->gobble(in);
+ nIters += thisIters;
- gobble(tempInFile);
+ for (int i = 0; i < size; i++) {
+ int tempCount;
+ in >> tempCount; m->gobble(in);
+ map<int, vector<double> >::iterator it = results.find(tempCount);
+ if (it != results.end()) {
+ for (int j = 0; j < thisIters; j++) {
+ double value;
+ in >> value; m->gobble(in);
+ (it->second).push_back(value);
+ }
+ }else {
+ vector<double> tempValues;
+ for (int j = 0; j < thisIters; j++) {
+ double value;
+ in >> value; m->gobble(in);
+ tempValues.push_back(value);
+ }
+ results[tempCount] = tempValues;
+ }
}
- tempInFile.close();
-
- remove(tempInName.c_str());
- remove(tempOutName.c_str());
-
- nIters = 1;
- output->resetFile();
+
+ in.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function close. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "RareDisplay", "inputTempFiles");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the RareDisplay class function close. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+/***********************************************************************/
+
+void RareDisplay::outputTempFiles(string filename){
+ try {
+ ofstream out;
+ m->openOutputFile(filename, out);
+
+ out << nIters-1 << '\t' << results.size() << endl;
+
+ for (map<int, vector<double> >::iterator it = results.begin(); it != results.end(); it++) {
+ out << it->first << '\t';
+ for(int i = 0; i < (it->second).size(); i++) {
+ out << (it->second)[i] << '\t';
+ }
+ out << endl;
+ }
+
+ out.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareDisplay", "outputTempFiles");
exit(1);
}
}
+
/***********************************************************************/
projects / mothur.git / blobdiff