+++ /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();
- m->mothurRemove(outName);
-}
-
-/***********************************************************************/
-
-void ThreeColumnFile::initFile(string label){
- try {
- if(counter != 0){
- m->openOutputFile(outName, outFile);
- m->openInputFile(inName, inFile);
-
- string inputBuffer;
- inputBuffer = m->getline(inFile);
-
- outFile << inputBuffer << '\t' << label << "\tlci\thci" << endl;
- }
- else{
- m->openOutputFile(outName, outFile);
- outFile << "numsampled\t" << label << "\tlci\thci" << endl;
- }
-
- outFile.setf(ios::fixed, ios::floatfield);
- outFile.setf(ios::showpoint);
- }
- catch(exception& e) {
- m->errorOut(e, "ThreeColumnFile", "initFile");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void ThreeColumnFile::output(int nSeqs, vector<double> data){
- try {
- if(counter != 0){
- string inputBuffer;
- inputBuffer = m->getline(inFile);
-
- 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) {
- m->errorOut(e, "ThreeColumnFile", "output");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void ThreeColumnFile::resetFile(){
- try {
- if(counter != 0){
- outFile.close();
- inFile.close();
- }
- else{
- outFile.close();
- }
- counter = 1;
-
- m->mothurRemove(inName);
- renameOk = rename(outName.c_str(), inName.c_str());
-
- //renameFile(outName, inName);
-
- //checks to make sure user was able to rename and remove successfully
- if ((renameOk != 0)) {
- m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
- perror(" : ");
- }
- }
- catch(exception& e) {
- m->errorOut(e, "ThreeColumnFile", "resetFile");
- exit(1);
- }
-}
-
-/***********************************************************************/
-/***********************************************************************/
-
-ColumnFile::~ColumnFile(){
-
- inFile.close();
- outFile.close();
- m->mothurRemove(outName);
-}
-
-/***********************************************************************/
-
-void ColumnFile::initFile(string label, vector<string> tags){
- try {
- if(counter != 0){
- m->openOutputFile(outName, outFile);
- m->openInputFile(inName, inFile);
-
- string inputBuffer;
- inputBuffer = m->getline(inFile);
-
- outFile << inputBuffer << '\t';
- for(int i = 0; i < tags.size(); i++) {
- outFile << label + tags[i] << '\t';
- }
- outFile << endl;
- }
- else{
- m->openOutputFile(outName, outFile);
- for(int i = 0; i < tags.size(); i++) {
- outFile << label + tags[i] << '\t';
- }
- outFile << endl;
- }
-
- outFile.setf(ios::fixed, ios::floatfield);
- outFile.setf(ios::showpoint);
- }
- catch(exception& e) {
- m->errorOut(e, "ColumnFile", "initFile");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void ColumnFile::output(vector<double> data){
- try {
-
- if(counter != 0){
- string inputBuffer;
- inputBuffer = m->getline(inFile);
-
- outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(iters.length());
- for (int i = 1; i< data.size(); i++) {
- outFile << '\t' << data[i];
- }
- outFile << endl;
- }
- else{
- outFile << setprecision(6) << data[0] << setprecision(iters.length());
- for (int i = 1; i< data.size(); i++) {
- outFile << '\t' << data[i];
- }
- outFile << endl;
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "ColumnFile", "output");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void ColumnFile::resetFile(){
- try {
- if(counter != 0){
- outFile.close();
- inFile.close();
- }
- else{
- outFile.close();
- }
- counter = 1;
-
- m->mothurRemove(inName);
- renameOk = rename(outName.c_str(), inName.c_str());
-
- //renameFile(outName, inName);
-
- //checks to make sure user was able to rename and remove successfully
- if ((renameOk != 0)) {
- m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
- perror(" : ");
- }
- }
- catch(exception& e) {
- m->errorOut(e, "ColumnFile", "resetFile");
- exit(1);
- }
-}
-
-/***********************************************************************/
-/***********************************************************************/
-
-SharedThreeColumnFile::~SharedThreeColumnFile(){
-
- inFile.close();
- outFile.close();
- m->mothurRemove(outName);
-}
-
-/***********************************************************************/
-
-void SharedThreeColumnFile::initFile(string label){
- try {
- if(counter != 0){
- m->openOutputFile(outName, outFile);
- m->openInputFile(inName, inFile);
-
- string inputBuffer;
- inputBuffer = m->getline(inFile);
-
- outFile << inputBuffer << '\t' << label << "\tlci\thci" << endl;
- }
- else{
- m->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) {
- m->errorOut(e, "SharedThreeColumnFile", "initFile");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
- try {
- if(counter != 0){
- string inputBuffer;
- inputBuffer = m->getline(inFile);
-
- 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) {
- m->errorOut(e, "SharedThreeColumnFile", "output");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void SharedThreeColumnFile::resetFile(){
- try {
- if(counter != 0){
- outFile.close();
- inFile.close();
- }
- else{
- outFile.close();
- }
- counter = 1;
-
- m->mothurRemove(inName);
- renameOk = rename(outName.c_str(), inName.c_str());
-
- //renameFile(outName, inName);
-
- //checks to make sure user was able to rename and remove successfully
- if ((renameOk != 0)) {
- m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
- perror(" : ");
- }
- }
- catch(exception& e) {
- m->errorOut(e, "SharedThreeColumnFile", "resetFile");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-/***********************************************************************/
-
-OneColumnFile::~OneColumnFile(){
-
- inFile.close();
- outFile.close();
- m->mothurRemove(outName);
-}
-
-/***********************************************************************/
-
-void OneColumnFile::initFile(string label){
- try {
- if(counter != 0){
- m->openOutputFile(outName, outFile);
- m->openInputFile(inName, inFile);
-
- string inputBuffer;
- inputBuffer = m->getline(inFile);
-
- outFile << inputBuffer << '\t' << label << endl;
- }
- else{
- m->openOutputFile(outName, outFile);
- outFile << "numsampled\t" << label << endl;
- }
-
- outFile.setf(ios::fixed, ios::floatfield);
- outFile.setf(ios::showpoint);
- }
- catch(exception& e) {
- m->errorOut(e, "OneColumnFile", "initFile");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void OneColumnFile::output(int nSeqs, vector<double> data){
- try {
- if(counter != 0){
- string inputBuffer;
- inputBuffer = m->getline(inFile);
-
- outFile << inputBuffer << setprecision(4) << '\t' << data[0] << endl;
- }
- else{
- outFile << nSeqs << setprecision(4) << '\t' << data[0] << endl;
- }
- }
- catch(exception& e) {
- m->errorOut(e, "OneColumnFile", "output");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void OneColumnFile::resetFile(){
- try {
- if(counter != 0){
- outFile.close();
- inFile.close();
- }else{
- outFile.close();
- }
- counter = 1;
-
- m->mothurRemove(inName);
- renameOk = rename(outName.c_str(), inName.c_str());
-
- //renameFile(outName, inName);
-
- //checks to make sure user was able to rename and remove successfully
- if ((renameOk != 0)) {
- m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
- perror(" : ");
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "OneColumnFile", "resetFile");
- exit(1);
- }
-}
-
-/***********************************************************************/
-/***********************************************************************/
-
-SharedOneColumnFile::~SharedOneColumnFile(){
-
- inFile.close();
- outFile.close();
- m->mothurRemove(outName);
-}
-
-/***********************************************************************/
-
-void SharedOneColumnFile::initFile(string label){
- try {
- if(counter != 0){
- m->openOutputFile(outName, outFile);
- m->openInputFile(inName, inFile);
-
- string inputBuffer;
- inputBuffer = m->getline(inFile);
-
- outFile << inputBuffer << '\t' << label << endl;
-
- }
- else{
- m->openOutputFile(outName, outFile);
- outFile << "sampled\t" << label << endl;
-
- }
-
- outFile.setf(ios::fixed, ios::floatfield);
- outFile.setf(ios::showpoint);
- }
- catch(exception& e) {
- m->errorOut(e, "SharedOneColumnFile", "initFile");
- 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;
- inputBuffer = m->getline(inFile);
-
- outFile << inputBuffer << setprecision(2) << '\t' << dataOutput << endl;
- }
- else{
- outFile << nSeqs << setprecision(2) << '\t' << dataOutput << endl;
- }
- }
- catch(exception& e) {
- m->errorOut(e, "SharedOneColumnFile", "output");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void SharedOneColumnFile::resetFile(){
- try {
- if(counter != 0){
- outFile.close();
- inFile.close();
- }
- else{
- outFile.close();
- }
- counter = 1;
-
- m->mothurRemove(inName);
- renameOk = rename(outName.c_str(), inName.c_str());
-
- //renameFile(outName, inName);
-
- //checks to make sure user was able to rename and remove successfully
- if ((renameOk != 0)) {
- m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
- perror(" : ");
- }
- }
- catch(exception& e) {
- m->errorOut(e, "SharedOneColumnFile", "resetFile");
- exit(1);
- }
-}
-
-/***********************************************************************/
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