fixed memory leak in parsimony calculator and added progress bars to parsimony and...

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 59cfb66fcc3d0f3e7136eabfebeacb4cd419d76c..da1d1bbb614ffd78f03484c3ca956e3f5aba21ac 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -228,6 +228,11 @@ bool ErrorCheck::checkInput(string input) {
                                 cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap or venn commands." << endl; return false; 
                        }
                }
+               
+               if ((commandName == "bin.seqs")) { 
+                       if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs command." << endl; return false; }
+                       validateBinFiles();
+               }
 
                return errorFree;
 }
@@ -470,6 +475,52 @@ void ErrorCheck::validateReadPhil() {
 }
 /*******************************************************/
 
+/******************************************************/
+//This function checks to make sure the user entered appropriate
+// format parameters on a bin.seq command
+void ErrorCheck::validateBinFiles() {
+       try {
+               ifstream filehandle;
+               int ableToOpen;
+               
+               if (fastafile == "") {
+                               cout << "fasta is a required parameter for bin.seqs." << endl; errorFree = false; 
+               }else if (fastafile != "") {
+                       //is it a valid filename'
+                       ableToOpen = openInputFile(fastafile, filehandle);
+                       filehandle.close();
+                       //unable to open
+                       if (ableToOpen == 1) {  errorFree = false; }
+               }else if (globaldata->getNameFile() != "") {
+                       //is it a valid filename'
+                       ifstream filehandle;
+                       int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle);
+                       filehandle.close();
+                       //unable to open
+                       if (ableToOpen == 1) {  errorFree = false; }
+               }else if (namefile != "") {
+                       //is it a valid filename'
+                       ifstream filehandle;
+                       int ableToOpen = openInputFile(namefile, filehandle);
+                       filehandle.close();
+                       //unable to open
+                       if (ableToOpen == 1) {  errorFree = false; }
+               }
+
+
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+
+/*******************************************************/
+
 /******************************************************/
 
 void ErrorCheck::clear() {