sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / fileoutput.cpp

diff --git a/fileoutput.cpp b/fileoutput.cpp
index 597a05a6ad9a892caff5f0b6f69269ae6af4013d..a4a68a8ef25a66ca52052faf8a1e8e6221bec4af 100644 (file)
--- a/fileoutput.cpp
+++ b/fileoutput.cpp
@@ -15,7 +15,7 @@ ThreeColumnFile::~ThreeColumnFile(){
        
        inFile.close();
        outFile.close();
-       remove(outName.c_str());
+       m->mothurRemove(outName);
 }
 
 /***********************************************************************/
@@ -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);
        }
 }
@@ -78,15 +78,19 @@ void ThreeColumnFile::resetFile(){
                }
                counter = 1;
                
-               remove(inName.c_str());
+               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)) {  mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
-
+               if ((renameOk != 0)) { 
+                       m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+                       perror(" : ");
+               }       
        }
        catch(exception& e) {
-               errorOut(e, "ThreeColumnFile", "resetFile");
+               m->errorOut(e, "ThreeColumnFile", "resetFile");
                exit(1);
        }
 }
@@ -98,7 +102,7 @@ ColumnFile::~ColumnFile(){
        
        inFile.close();
        outFile.close();
-       remove(outName.c_str());
+       m->mothurRemove(outName);
 }
 
 /***********************************************************************/
@@ -106,11 +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++) {
@@ -119,7 +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';
                        }
@@ -130,7 +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);
        }
 }
@@ -142,7 +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++) {
@@ -160,7 +164,7 @@ void ColumnFile::output(vector<double> data){
 
        }
        catch(exception& e) {
-               errorOut(e, "ColumnFile", "output");
+               m->errorOut(e, "ColumnFile", "output");
                exit(1);
        }
 }
@@ -178,15 +182,19 @@ void ColumnFile::resetFile(){
                }
                counter = 1;
                
-               remove(inName.c_str());
+               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)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
-
+               if ((renameOk != 0)) { 
+                       m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+                       perror(" : ");
+               }       
        }
        catch(exception& e) {
-               errorOut(e, "ColumnFile", "resetFile");
+               m->errorOut(e, "ColumnFile", "resetFile");
                exit(1);
        }
 }
@@ -198,7 +206,7 @@ SharedThreeColumnFile::~SharedThreeColumnFile(){
        
        inFile.close();
        outFile.close();
-       remove(outName.c_str());
+       m->mothurRemove(outName);
 }
 
 /***********************************************************************/
@@ -206,16 +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;
                }
 
@@ -223,7 +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);
        }
 }
@@ -234,7 +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;
                }
@@ -244,7 +252,7 @@ void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
                }
        }
        catch(exception& e) {
-               errorOut(e, "SharedThreeColumnFile", "output");
+               m->errorOut(e, "SharedThreeColumnFile", "output");
                exit(1);
        }
 }
@@ -261,15 +269,20 @@ void SharedThreeColumnFile::resetFile(){
                        outFile.close();
                }
                counter = 1;
-               remove(inName.c_str());
+               
+               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)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
-
+               if ((renameOk != 0)) { 
+                       m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+                       perror(" : ");
+               }       
        }
        catch(exception& e) {
-               errorOut(e, "SharedThreeColumnFile", "resetFile");
+               m->errorOut(e, "SharedThreeColumnFile", "resetFile");
                exit(1);
        }
 }
@@ -282,7 +295,7 @@ OneColumnFile::~OneColumnFile(){
        
        inFile.close();
        outFile.close();
-       remove(outName.c_str());        
+       m->mothurRemove(outName);       
 }
 
 /***********************************************************************/
@@ -290,24 +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);
        }
 }
@@ -318,7 +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;
                }
@@ -327,7 +340,7 @@ void OneColumnFile::output(int nSeqs, vector<double> data){
                }
        }
        catch(exception& e) {
-               errorOut(e, "OneColumnFile", "output");
+               m->errorOut(e, "OneColumnFile", "output");
                exit(1);
        }
 }
@@ -339,20 +352,25 @@ void OneColumnFile::resetFile(){
                if(counter != 0){
                        outFile.close();
                        inFile.close();
-               }
-               else{
+               }else{
                        outFile.close();
                }       
                counter = 1;
-               remove(inName.c_str());
+               
+               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)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
+               if ((renameOk != 0)) { 
+                       m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+                       perror(" : ");
+               }       
 
        }
        catch(exception& e) {
-               errorOut(e, "OneColumnFile", "resetFile");
+               m->errorOut(e, "OneColumnFile", "resetFile");
                exit(1);
        }
 }
@@ -364,7 +382,7 @@ SharedOneColumnFile::~SharedOneColumnFile(){
        
        inFile.close();
        outFile.close();
-       remove(outName.c_str());        
+       m->mothurRemove(outName);       
 }
 
 /***********************************************************************/
@@ -372,17 +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;
                
                }
@@ -391,7 +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);
        }
 }
@@ -409,7 +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;
                        }
@@ -418,7 +436,7 @@ void SharedOneColumnFile::output(int nSeqs, vector<double> data){
                        }
        }
        catch(exception& e) {
-               errorOut(e, "SharedOneColumnFile", "output");
+               m->errorOut(e, "SharedOneColumnFile", "output");
                exit(1);
        }
 }
@@ -435,17 +453,20 @@ void SharedOneColumnFile::resetFile(){
                        outFile.close();
                }       
                counter = 1;
-               
-               remove(inName.c_str());
+
+               m->mothurRemove(inName);
                renameOk = rename(outName.c_str(), inName.c_str());
                
-               //checks to make sure user was able to rename and remove successfully
-               if ((renameOk != 0)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
-
+               //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) {
-               errorOut(e, "SharedOneColumnFile", "resetFile");
+               m->errorOut(e, "SharedOneColumnFile", "resetFile");
                exit(1);
        }
 }