a few modifications for 1.9

[mothur.git] / fileoutput.cpp

diff --git a/fileoutput.cpp b/fileoutput.cpp
index cd3a1c74084de46dd7f5c7805d3425f0d0dd3ecb..117f8ab1c3a9a93c5f80f38613c4aefa1c898e32 100644 (file)
--- a/fileoutput.cpp
+++ b/fileoutput.cpp
@@ -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);
        }
 }
@@ -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);
        }
 }
@@ -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);
        }
 }
@@ -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);
        }
 }
@@ -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);
        }
 }
@@ -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);
        }
 }
@@ -313,7 +320,7 @@ void OneColumnFile::initFile(string label){
                outFile.setf(ios::showpoint);
        }
        catch(exception& e) {
-               errorOut(e, "OneColumnFile", "initFile");
+               m->errorOut(e, "OneColumnFile", "initFile");
                exit(1);
        }
 }
@@ -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);
        }
 }
@@ -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);
        }
 }
@@ -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);
        }
 }