--- /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);
+ }
+}
+
+/***********************************************************************/
projects / mothur.git / blobdiff