added get.otus and remove.otus commands

[mothur.git] / fileoutput.cpp

diff --git a/fileoutput.cpp b/fileoutput.cpp
index 004ed8313511c2dd42d4b87aca93c0ad5750bce5..c2432acaaf039b9ef9ac59b287cd55649f606105 100644 (file)
--- a/fileoutput.cpp
+++ b/fileoutput.cpp
@@ -23,16 +23,16 @@ ThreeColumnFile::~ThreeColumnFile(){
 void ThreeColumnFile::initFile(string label){
        try {
                if(counter != 0){
-                       openOutputFile(outName, outFile);
-                       openInputFile(inName, inFile);
+                       m->openOutputFile(outName, outFile);
+                       m->openInputFile(inName, inFile);
 
                        string inputBuffer;
-                       inputBuffer = getline(inFile);
+                       inputBuffer = m->getline(inFile);
                
                        outFile <<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
                }
                else{
-                       openOutputFile(outName, outFile);
+                       m->openOutputFile(outName, outFile);
                        outFile << "numsampled\t" << label << "\tlci\thci" << endl;
                }
 
@@ -40,7 +40,7 @@ void ThreeColumnFile::initFile(string label){
                outFile.setf(ios::showpoint);
        }
        catch(exception& e) {
-               errorOut(e, "ThreeColumnFile", "initFile");
+               m->errorOut(e, "ThreeColumnFile", "initFile");
                exit(1);
        }
 }
@@ -51,7 +51,7 @@ void ThreeColumnFile::output(int nSeqs, vector<double> data){
        try {
                if(counter != 0){               
                        string inputBuffer;
-                       inputBuffer = getline(inFile);
+                       inputBuffer = m->getline(inFile);
                
                        outFile <<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
                }
@@ -60,7 +60,7 @@ void ThreeColumnFile::output(int nSeqs, vector<double> data){
                }
        }
        catch(exception& e) {
-               errorOut(e, "ThreeColumnFile", "output");
+               m->errorOut(e, "ThreeColumnFile", "output");
                exit(1);
        }
 }
@@ -81,14 +81,16 @@ void ThreeColumnFile::resetFile(){
                remove(inName.c_str());
                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)) { 
-                       mothurOut("Unable to rename " + outName); mothurOutEndLine();
+                       m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
                        perror(" : ");
                }       
        }
        catch(exception& e) {
-               errorOut(e, "ThreeColumnFile", "resetFile");
+               m->errorOut(e, "ThreeColumnFile", "resetFile");
                exit(1);
        }
 }
@@ -108,11 +110,11 @@ ColumnFile::~ColumnFile(){
 void ColumnFile::initFile(string label, vector<string> tags){
        try {
                if(counter != 0){
-                       openOutputFile(outName, outFile);
-                       openInputFile(inName, inFile);
+                       m->openOutputFile(outName, outFile);
+                       m->openInputFile(inName, inFile);
 
                        string inputBuffer;
-                       inputBuffer = getline(inFile);
+                       inputBuffer = m->getline(inFile);
                
                        outFile <<  inputBuffer << '\t'; 
                        for(int i = 0; i < tags.size(); i++) {
@@ -121,7 +123,7 @@ void ColumnFile::initFile(string label, vector<string> tags){
                        outFile << endl;
                }
                else{
-                       openOutputFile(outName, outFile);
+                       m->openOutputFile(outName, outFile);
                        for(int i = 0; i < tags.size(); i++) {
                                outFile << label + tags[i] << '\t';
                        }
@@ -132,7 +134,7 @@ void ColumnFile::initFile(string label, vector<string> tags){
                outFile.setf(ios::showpoint);
        }
        catch(exception& e) {
-               errorOut(e, "ColumnFile", "initFile");
+               m->errorOut(e, "ColumnFile", "initFile");
                exit(1);
        }
 }
@@ -144,7 +146,7 @@ void ColumnFile::output(vector<double> data){
        
                if(counter != 0){               
                        string inputBuffer;
-                       inputBuffer = getline(inFile);
+                       inputBuffer = m->getline(inFile);
 
                        outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(iters.length());
                        for (int i = 1; i< data.size(); i++) {
@@ -162,7 +164,7 @@ void ColumnFile::output(vector<double> data){
 
        }
        catch(exception& e) {
-               errorOut(e, "ColumnFile", "output");
+               m->errorOut(e, "ColumnFile", "output");
                exit(1);
        }
 }
@@ -183,14 +185,16 @@ void ColumnFile::resetFile(){
                remove(inName.c_str());
                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)) { 
-                       mothurOut("Unable to rename " + outName); mothurOutEndLine();
+                       m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
                        perror(" : ");
                }       
        }
        catch(exception& e) {
-               errorOut(e, "ColumnFile", "resetFile");
+               m->errorOut(e, "ColumnFile", "resetFile");
                exit(1);
        }
 }
@@ -210,16 +214,16 @@ SharedThreeColumnFile::~SharedThreeColumnFile(){
 void SharedThreeColumnFile::initFile(string label){
        try {
                if(counter != 0){
-                       openOutputFile(outName, outFile);
-                       openInputFile(inName, inFile);
+                       m->openOutputFile(outName, outFile);
+                       m->openInputFile(inName, inFile);
 
                        string inputBuffer;
-                       inputBuffer = getline(inFile);
+                       inputBuffer = m->getline(inFile);
                
                        outFile <<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
                }
                else{
-                       openOutputFile(outName, outFile);
+                       m->openOutputFile(outName, outFile);
                        outFile << "numsampled\t" << groupLabel << '\t' << label << "\tlci\thci" << endl;
                }
 
@@ -227,7 +231,7 @@ void SharedThreeColumnFile::initFile(string label){
                outFile.setf(ios::showpoint);
        }
        catch(exception& e) {
-               errorOut(e, "SharedThreeColumnFile", "initFile");
+               m->errorOut(e, "SharedThreeColumnFile", "initFile");
                exit(1);
        }
 }
@@ -238,7 +242,7 @@ void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
        try {
                if(counter != 0){               
                        string inputBuffer;
-                       inputBuffer = getline(inFile);
+                       inputBuffer = m->getline(inFile);
                
                        outFile <<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
                }
@@ -248,7 +252,7 @@ void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
                }
        }
        catch(exception& e) {
-               errorOut(e, "SharedThreeColumnFile", "output");
+               m->errorOut(e, "SharedThreeColumnFile", "output");
                exit(1);
        }
 }
@@ -265,17 +269,20 @@ void SharedThreeColumnFile::resetFile(){
                        outFile.close();
                }
                counter = 1;
+               
                remove(inName.c_str());
                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)) { 
-                       mothurOut("Unable to rename " + outName); mothurOutEndLine();
+                       m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
                        perror(" : ");
                }       
        }
        catch(exception& e) {
-               errorOut(e, "SharedThreeColumnFile", "resetFile");
+               m->errorOut(e, "SharedThreeColumnFile", "resetFile");
                exit(1);
        }
 }
@@ -296,24 +303,24 @@ OneColumnFile::~OneColumnFile(){
 void OneColumnFile::initFile(string label){
        try {
                if(counter != 0){
-                       openOutputFile(outName, outFile);
-                       openInputFile(inName, inFile);
+                       m->openOutputFile(outName, outFile);
+                       m->openInputFile(inName, inFile);
                
                        string inputBuffer;
-                       inputBuffer = getline(inFile);
+                       inputBuffer = m->getline(inFile);
                
                        outFile <<  inputBuffer << '\t' << label << endl;
                }
                else{
-                       openOutputFile(outName, outFile);
-                       outFile << "numsequences\t" << label << endl;
+                       m->openOutputFile(outName, outFile);
+                       outFile << "numsampled\t" << label << endl;
                }
        
                outFile.setf(ios::fixed, ios::floatfield);
                outFile.setf(ios::showpoint);
        }
        catch(exception& e) {
-               errorOut(e, "OneColumnFile", "initFile");
+               m->errorOut(e, "OneColumnFile", "initFile");
                exit(1);
        }
 }
@@ -324,7 +331,7 @@ void OneColumnFile::output(int nSeqs, vector<double> data){
        try {   
                if(counter != 0){               
                        string inputBuffer;
-                       inputBuffer = getline(inFile);
+                       inputBuffer = m->getline(inFile);
                
                        outFile <<  inputBuffer << setprecision(4) << '\t'  << data[0] << endl;
                }
@@ -333,7 +340,7 @@ void OneColumnFile::output(int nSeqs, vector<double> data){
                }
        }
        catch(exception& e) {
-               errorOut(e, "OneColumnFile", "output");
+               m->errorOut(e, "OneColumnFile", "output");
                exit(1);
        }
 }
@@ -345,22 +352,25 @@ void OneColumnFile::resetFile(){
                if(counter != 0){
                        outFile.close();
                        inFile.close();
-               }
-               else{
+               }else{
                        outFile.close();
                }       
                counter = 1;
+               
                remove(inName.c_str());
                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)) { 
-                       mothurOut("Unable to rename " + outName); mothurOutEndLine();
+                       m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
                        perror(" : ");
                }       
+
        }
        catch(exception& e) {
-               errorOut(e, "OneColumnFile", "resetFile");
+               m->errorOut(e, "OneColumnFile", "resetFile");
                exit(1);
        }
 }
@@ -380,17 +390,17 @@ SharedOneColumnFile::~SharedOneColumnFile(){
 void SharedOneColumnFile::initFile(string label){
        try {
                if(counter != 0){
-                       openOutputFile(outName, outFile);
-                       openInputFile(inName, inFile);
+                       m->openOutputFile(outName, outFile);
+                       m->openInputFile(inName, inFile);
                
                        string inputBuffer;
-                       inputBuffer = getline(inFile);
+                       inputBuffer = m->getline(inFile);
                
                        outFile <<  inputBuffer << '\t' << label  << endl;
 
                }
                else{
-                       openOutputFile(outName, outFile);
+                       m->openOutputFile(outName, outFile);
                        outFile << "sampled\t" << label << endl;
                
                }
@@ -399,7 +409,7 @@ void SharedOneColumnFile::initFile(string label){
                outFile.setf(ios::showpoint);
        }
        catch(exception& e) {
-               errorOut(e, "SharedOneColumnFile", "initFile");
+               m->errorOut(e, "SharedOneColumnFile", "initFile");
                exit(1);
        }
 }
@@ -417,7 +427,7 @@ void SharedOneColumnFile::output(int nSeqs, vector<double> data){
                        }
                        if(counter != 0){               
                                string inputBuffer;
-                               inputBuffer = getline(inFile);
+                               inputBuffer = m->getline(inFile);
 
                                outFile <<  inputBuffer << setprecision(2) << '\t' << dataOutput << endl;
                        }
@@ -426,7 +436,7 @@ void SharedOneColumnFile::output(int nSeqs, vector<double> data){
                        }
        }
        catch(exception& e) {
-               errorOut(e, "SharedOneColumnFile", "output");
+               m->errorOut(e, "SharedOneColumnFile", "output");
                exit(1);
        }
 }
@@ -445,17 +455,18 @@ void SharedOneColumnFile::resetFile(){
                counter = 1;
 
                remove(inName.c_str());
-
                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)) { 
-                       mothurOut("Unable to rename " + outName); mothurOutEndLine();
+                       m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
                        perror(" : ");
                }       
        }
        catch(exception& e) {
-               errorOut(e, "SharedOneColumnFile", "resetFile");
+               m->errorOut(e, "SharedOneColumnFile", "resetFile");
                exit(1);
        }
 }