namefile = globaldata->getNameFile();
groupfile = globaldata->getGroupFile();
orderfile = globaldata->getOrderFile();
+ fastafile = globaldata->getFastaFile();
+ treefile = globaldata->getTreeFile();
cutoff = globaldata->getCutOff();
format = globaldata->getFormat();
method = globaldata->getMethod();
//is it a valid parameter
if (validParameter->isValidParameter(parameter) != true) { return false; }
- if (parameter == "phylipfile" ) { phylipfile = value; }
- if (parameter == "columnfile" ) { columnfile = value; }
- if (parameter == "listfile" ) { listfile = value; }
- if (parameter == "rabundfile" ) { rabundfile = value; }
- if (parameter == "sabundfile" ) { sabundfile = value; }
- if (parameter == "namefile" ) { namefile = value; }
- if (parameter == "orderfile" ) { orderfile = value; }
- if (parameter == "groupfile" ) { groupfile = value; }
+ if (parameter == "phylip" ) { phylipfile = value; }
+ if (parameter == "column" ) { columnfile = value; }
+ if (parameter == "list" ) { listfile = value; }
+ if (parameter == "rabund" ) { rabundfile = value; }
+ if (parameter == "sabund" ) { sabundfile = value; }
+ if (parameter == "name" ) { namefile = value; }
+ if (parameter == "order" ) { orderfile = value; }
+ if (parameter == "fasta" ) { fastafile = value; }
+ if (parameter == "treefile" ) { treefile = value; }
+ if (parameter == "group" ) { groupfile = value; }
if (parameter == "cutoff" ) { cutoff = value; }
if (parameter == "precision" ) { precision = value; }
if (parameter == "iters" ) { iters = value; }
//is it a valid parameter
if (validParameter->isValidParameter(parameter) != true) { return false; }
- if (parameter == "phylipfile" ) { phylipfile = value; }
- if (parameter == "columnfile" ) { columnfile = value; }
- if (parameter == "listfile" ) { listfile = value; }
- if (parameter == "rabundfile" ) { rabundfile = value; }
- if (parameter == "sabundfile" ) { sabundfile = value; }
- if (parameter == "namefile" ) { namefile = value; }
- if (parameter == "orderfile" ) { orderfile = value; }
- if (parameter == "groupfile" ) { groupfile = value; }
+ if (parameter == "phylip" ) { phylipfile = value; }
+ if (parameter == "column" ) { columnfile = value; }
+ if (parameter == "list" ) { listfile = value; }
+ if (parameter == "rabund" ) { rabundfile = value; }
+ if (parameter == "sabund" ) { sabundfile = value; }
+ if (parameter == "name" ) { namefile = value; }
+ if (parameter == "order" ) { orderfile = value; }
+ if (parameter == "group" ) { groupfile = value; }
+ if (parameter == "fasta" ) { fastafile = value; }
+ if (parameter == "treefile" ) { treefile = value; }
if (parameter == "cutoff" ) { cutoff = value; }
if (parameter == "precision" ) { precision = value; }
if (parameter == "iters" ) { iters = value; }
validateReadFiles();
validateReadDist();
}else if (commandName == "read.otu") {
+ //you want to do shared commands
+ if ((listfile != "") && (groupfile != "")) {
+ validateParseFiles(); //checks the listfile and groupfile parameters
+ }else { //you want to do single commands
+ validateReadFiles();
+ validateReadPhil();
+ }
+ }else if (commandName == "read.tree") {
+ validateTreeFiles(); //checks the treefile and groupfile parameters
+ }else if (commandName == "deconvolute") {
+ if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
validateReadFiles();
- validateReadPhil();
- }else if (commandName == "read.list") {
- validateParseFiles(); //checks the listfile and groupfile parameters
}
//are you trying to cluster before you have read something
}
if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a listfile, sabundfile or rabundfile before you can use the collect.single, rarefaction.single or summary.single commands." << endl; return false; }
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the collect.single, rarefaction.single or summary.single commands." << endl; return false; }
}
- if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "shared") ){
- if (globaldata->getListFile() == "") { cout << "You must read a listfile and a groupfile before you can use the collect.shared, rarefaction.shared, summary.shared or shared commands." << endl; return false; }
- else if (globaldata->getGroupFile() == "") { cout << "You must read a listfile and a groupfile before you can use the collect.shared, rarefaction.shared, summary.shared or shared commands." << endl; return false; }
+ if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){
+ if (globaldata->getListFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
+ else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
}
//unable to open
if (ableToOpen == 1) { errorFree = false; }
else { globaldata->inputFileName = sabundfile; }
+ }else if (fastafile != "") {
+ ableToOpen = openInputFile(fastafile, filehandle);
+ filehandle.close();
+ //unable to open
+ if (ableToOpen == 1) { errorFree = false; }
+ else { globaldata->inputFileName = fastafile; }
}else{ //no file given
errorFree = false;
}
ifstream filehandle;
int ableToOpen;
- if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylipfile or a columnfile." << endl; errorFree = false; }
- else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylipfile or columnfile." << endl; errorFree = false; }
+ if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
+ else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
if (columnfile != "") {
if (namefile == "") {
- cout << "You need to provide a namefile name if you are going to use the column format." << endl;
+ cout << "You need to provide a namefile if you are going to use the column format." << endl;
errorFree = false;
}else {
ableToOpen = openInputFile(namefile, filehandle);
//checks for valid files
- if (listfile == "") { cout << "When executing a read.list you must enter a listfile and a groupfile." << endl; errorFree = false; }
- else if (groupfile == "") { cout << "When executing a read.list you must enter a listfile and a groupfile." << endl; errorFree = false; }
+ if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
+ else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
//checks parameters on the read command
if (listfile != "") {
exit(1);
}
}
+/*******************************************************/
+
+/******************************************************/
+//This function checks to make sure the user entered appropriate
+// format parameters on a parselistcommand
+void ErrorCheck::validateTreeFiles() {
+ try {
+ ifstream filehandle;
+ int ableToOpen;
+
+ //checks for valid files
+
+ if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
+ else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
+
+ //checks parameters on the read command
+ if (treefile != "") {
+ ableToOpen = openInputFile(treefile, filehandle);
+ filehandle.close();
+ if (ableToOpen == 1) { //unable to open
+ errorFree = false;
+ }
+ if (groupfile != "") {
+ ableToOpen = openInputFile(groupfile, filehandle);
+ filehandle.close();
+ if (ableToOpen == 1) { //unable to open
+ errorFree = false;;
+ }
+ }
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
/*******************************************************/
//checks to make sure only one file type is given
if (listfile != "") {
if ((rabundfile != "") || (sabundfile != "")) {
- cout << "When executing a read.otu you must enter ONLY ONE of the following: listfile, rabundfile or sabundfile." << endl; errorFree = false; }
+ cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
}else if (rabundfile != "") {
if ((listfile != "") || (sabundfile != "")) {
- cout << "When executing a read.otu you must enter ONLY ONE of the following: listfile, rabundfile or sabundfile." << endl; errorFree = false; }
+ cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
}else if (sabundfile != "") {
if ((listfile != "") || (rabundfile != "")) {
- cout << "When executing a read.otu you must enter ONLY ONE of the following: listfile, rabundfile or sabundfile." << endl; errorFree = false; }
+ cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
}else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
- cout << "When executing a read.otu you must enter one of the following: listfile, rabundfile or sabundfile." << endl; errorFree = false;
+ cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
}
//checks parameters on the read command
projects / mothur.git / blobdiff