if (parameter == "label" ) { label = value; }
if (parameter == "abund" ) { abund = value; }
if (parameter == "random" ) { randomtree = value; }
+ if (parameter == "sorted" ) { sorted = value; }
}
//gets the last parameter and value
if (parameter == "label" ) { label = value; }
if (parameter == "random" ) { randomtree = value; }
if (parameter == "abund" ) { abund = value; }
+ if (parameter == "sorted" ) { sorted = value; }
}
}
}
}
- if (commandName == "heatmap"){
+ if ((commandName == "heatmap") || (commandName == "venn")) {
if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
- cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap command." << endl; return false;
+ 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();
+ }
+
+ if ((commandName == "get.oturep")) {
+ if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
+ cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl;
+ errorFree = false;
+ }
+ if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; }
+ validateBinFiles();
+ }
+
return errorFree;
}
}
/*******************************************************/
+/******************************************************/
+//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 and get.oturep commands." << 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 (listfile != "") {
+ //is it a valid filename'
+ ableToOpen = openInputFile(listfile, 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() {