--- /dev/null
+/*
+ * fileoutput.cpp
+ * Dotur
+ *
+ * Created by Sarah Westcott on 11/18/08.
+ * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "fileoutput.h"
+
+/***********************************************************************/
+
+ThreeColumnFile::~ThreeColumnFile(){
+
+ inFile.close();
+ outFile.close();
+ remove(outName.c_str());
+};
+
+/***********************************************************************/
+
+void ThreeColumnFile::initFile(string label){
+ try {
+ if(counter != 0){
+ openOutputFile(outName, outFile);
+ openInputFile(inName, inFile);
+
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ outFile << inputBuffer << '\t' << label << "\tlci\thci" << endl;
+ }
+ else{
+ openOutputFile(outName, outFile);
+ outFile << "numsampled\t" << label << "\tlci\thci" << endl;
+ }
+
+ outFile.setf(ios::fixed, ios::floatfield);
+ outFile.setf(ios::showpoint);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ThreeColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void ThreeColumnFile::output(int nSeqs, vector<double> data){
+ try {
+ if(counter != 0){
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ outFile << inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+ else{
+ outFile << nSeqs << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ThreeColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+};
+
+/***********************************************************************/
+
+void ThreeColumnFile::resetFile(){
+ try {
+ if(counter != 0){
+ outFile.close();
+ inFile.close();
+ }
+ else{
+ outFile.close();
+ }
+ counter = 1;
+ remove(inName.c_str());
+ rename(outName.c_str(), inName.c_str());
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ThreeColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+/***********************************************************************/
+
+SharedThreeColumnFile::~SharedThreeColumnFile(){
+
+ inFile.close();
+ outFile.close();
+ remove(outName.c_str());
+};
+
+/***********************************************************************/
+
+void SharedThreeColumnFile::initFile(string label){
+ try {
+ if(counter != 0){
+ openOutputFile(outName, outFile);
+ openInputFile(inName, inFile);
+
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ outFile << inputBuffer << '\t' << label << "\tlci\thci" << endl;
+ }
+ else{
+ openOutputFile(outName, outFile);
+ outFile << "numsampled\t" << groupLabel << '\t' << label << "\tlci\thci" << endl;
+ }
+
+ outFile.setf(ios::fixed, ios::floatfield);
+ outFile.setf(ios::showpoint);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SharedThreeColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
+ try {
+ if(counter != 0){
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ outFile << inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+ else{
+ outFile << numGroup << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+ numGroup++;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SharedThreeColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+};
+
+/***********************************************************************/
+
+void SharedThreeColumnFile::resetFile(){
+ try {
+ if(counter != 0){
+ outFile.close();
+ inFile.close();
+ }
+ else{
+ outFile.close();
+ }
+ counter = 1;
+ remove(inName.c_str());
+ rename(outName.c_str(), inName.c_str());
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SharedThreeColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+/***********************************************************************/
+
+OneColumnFile::~OneColumnFile(){
+
+ inFile.close();
+ outFile.close();
+ remove(outName.c_str());
+};
+
+/***********************************************************************/
+
+void OneColumnFile::initFile(string label){
+ try {
+ if(counter != 0){
+ openOutputFile(outName, outFile);
+ openInputFile(inName, inFile);
+
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ outFile << inputBuffer << '\t' << label << endl;
+ }
+ else{
+ openOutputFile(outName, outFile);
+ outFile << "numsequences\t" << label << endl;
+ }
+
+ outFile.setf(ios::fixed, ios::floatfield);
+ outFile.setf(ios::showpoint);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the OneColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void OneColumnFile::output(int nSeqs, vector<double> data){
+ try {
+ if(counter != 0){
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ outFile << inputBuffer << setprecision(4) << '\t' << data[0] << endl;
+ }
+ else{
+ outFile << nSeqs << setprecision(4) << '\t' << data[0] << endl;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the OneColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+};
+
+/***********************************************************************/
+
+void OneColumnFile::resetFile(){
+ try {
+ if(counter != 0){
+ outFile.close();
+ inFile.close();
+ }
+ else{
+ outFile.close();
+ }
+ counter = 1;
+ remove(inName.c_str());
+ rename(outName.c_str(), inName.c_str());
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the OneColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+/***********************************************************************/
+
+SharedOneColumnFile::~OneColumnFile(){
+
+ inFile.close();
+ outFile.close();
+ remove(outName.c_str());
+};
+
+/***********************************************************************/
+
+void SharedOneColumnFile::initFile(string label){
+ try {
+ if(counter != 0){
+ openOutputFile(outName, outFile);
+ openInputFile(inName, inFile);
+
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ outFile << inputBuffer << '\t' << label << endl;
+
+ }
+ else{
+ openOutputFile(outName, outFile);
+ outFile << "sampled\t" << label << endl;
+
+ }
+
+ outFile.setf(ios::fixed, ios::floatfield);
+ outFile.setf(ios::showpoint);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the OneColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void SharedOneColumnFile::output(int nSeqs, vector<double> data){
+ try {
+ string dataOutput;
+ float sam;
+ sam = data[0];
+ dataOutput = "";
+ for (int i = 0; i < data.size(); i++) {
+ dataOutput = dataOutput + "\t" + toString(data[i]);
+ }
+ if(counter != 0){
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ outFile << inputBuffer << setprecision(2) << '\t' << dataOutput << endl;
+ }
+ else{
+ outFile << nSeqs << setprecision(2) << '\t' << dataOutput << endl;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the OneColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+};
+
+/***********************************************************************/
+
+void SharedOneColumnFile::resetFile(){
+ try {
+ if(counter != 0){
+ outFile.close();
+ inFile.close();
+ }
+ else{
+ outFile.close();
+ }
+ counter = 1;
+ remove(inName.c_str());
+ rename(outName.c_str(), inName.c_str());
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the OneColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
projects / mothur.git / blobdiff