added remove.seqs command

[mothur.git] / raredisplay.cpp

diff --git a/raredisplay.cpp b/raredisplay.cpp
index 6843ebe61b1d6c2bd650a296d286c9a3ec92b0af..b86312bc4411e8cdd2faca9934aab3abf5c96c52 100644 (file)
--- a/raredisplay.cpp
+++ b/raredisplay.cpp
@@ -15,6 +15,7 @@ void RareDisplay::init(string label){
        try {
                this->label = label;
                if(nIters != 1){
+                       tempInFile.clear();
                        openOutputFile(tempOutName, tempOutFile);
                        openInputFile(tempInName, tempInFile);
                }
@@ -23,11 +24,7 @@ void RareDisplay::init(string label){
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function init. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the RareDisplay class function init. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "RareDisplay", "init");
                exit(1);
        }
 }
@@ -58,14 +55,10 @@ void RareDisplay::update(SAbundVector* rank){
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the RareDisplay class function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "RareDisplay", "update");
                exit(1);
        }
-};
+}
 
 /***********************************************************************/
 void RareDisplay::update(vector<SharedRAbundVector*> shared, int numSeqs, int numGroupComb) {
@@ -91,14 +84,10 @@ void RareDisplay::update(vector<SharedRAbundVector*> shared, int numSeqs, int nu
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the RareDisplay class function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "RareDisplay", "update");
                exit(1);
        }
-};
+}
 
 /***********************************************************************/
 
@@ -118,14 +107,10 @@ void RareDisplay::reset(){
                renameOk = rename(tempOutName.c_str(), tempInName.c_str());     
                
                //checks to make sure user was able to rename and remove successfully
-               if (renameOk != 0) { cout << "Unable to rename the necessary temp files." << endl; }
+               if (renameOk != 0) { mothurOut("Unable to rename the necessary temp files."); mothurOutEndLine(); }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function reset. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the RareDisplay class function reset. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "RareDisplay", "reset");
                exit(1);
        }
 }
@@ -166,11 +151,7 @@ void RareDisplay::close(){
                output->resetFile();
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function close. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the RareDisplay class function close. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "RareDisplay", "close");
                exit(1);
        }
 }