validCommand = new ValidCommands();
validParameter = new ValidParameters();
validCalculator = new ValidCalculators();
- distfile = globaldata->getDistFile();
+ columnfile = globaldata->getColumnFile();
+ phylipfile = globaldata->getPhylipFile();
listfile = globaldata->getListFile();
rabundfile = globaldata->getRabundFile();
sabundfile = globaldata->getSabundFile();
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 == "distfile" ) { distfile = 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 == "distfile" ) { distfile = 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; }
//make sure the user does not use both the line and label parameters
if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
+
- //validate files
- if (commandName == "parselist") {
- validateParseFiles(commandName);
- }
- if ((commandName == "read.phylip") || (commandName == "read.column")) {
+ if (commandName == "read.dist") {
validateReadFiles();
validateReadDist();
- }else if ((commandName == "read.list") || (commandName == "read.rabund") || (commandName == "read.sabund")){
- validateReadFiles();
- validateReadPhil(commandName);
- }else if (commandName == "read.shared") {
+ }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") {
validateReadFiles();
- validateParseFiles(commandName); //checks the listfile and groupfile parameters
}
//are you trying to cluster before you have read something
ifstream filehandle;
int ableToOpen;
- //are we reading a distfile
- if (distfile != "") {
- ableToOpen = openInputFile(distfile, filehandle);
+ //are we reading a phylipfile
+ if (phylipfile != "") {
+ ableToOpen = openInputFile(phylipfile, filehandle);
+ filehandle.close();
+ //unable to open
+ if (ableToOpen == 1) { errorFree = false; }
+ else { globaldata->inputFileName = phylipfile; }
+ //are we reading a phylipfile
+ }else if (columnfile != "") {
+ ableToOpen = openInputFile(columnfile, filehandle);
filehandle.close();
//unable to open
if (ableToOpen == 1) { errorFree = false; }
- else { globaldata->inputFileName = distfile; }
+ else { globaldata->inputFileName = columnfile; }
//are we reading a listfile
}else if (listfile!= "") {
ableToOpen = openInputFile(listfile, filehandle);
//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 (distfile == "") { cout << "When executing a read.phylip or read.column you must enter a distfile." << endl; errorFree = false; }
+ 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 (commandName == "read.column") {
+ if (columnfile != "") {
if (namefile == "") {
cout << "You need to provide a namefile name if you are going to use the column format." << endl;
errorFree = false;
/******************************************************/
//This function checks to make sure the user entered appropriate
// format parameters on a parselistcommand
-void ErrorCheck::validateParseFiles(string command) {
+void ErrorCheck::validateParseFiles() {
try {
ifstream filehandle;
int ableToOpen;
//checks for valid files
- if (command == "read.shared" ) {
- if (listfile == "") { cout << "When executing a read.shared you must enter a listfile and a groupfile." << endl; errorFree = false; }
- else if (groupfile == "") { cout << "When executing a read.shared you must enter a listfile and a groupfile." << endl; errorFree = false; }
- }else if (command == "parselist" ) {
- if (listfile == "") { cout << "When executing a parselist you must enter a listfile and a groupfile." << endl; errorFree = false; }
- else if (groupfile == "") { cout << "When executing a parselist you must enter a listfile and a groupfile." << endl; errorFree = false; }
- }
-
+
+ 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; }
+
//checks parameters on the read command
if (listfile != "") {
ableToOpen = openInputFile(listfile, filehandle);
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);
+ }
+}
/*******************************************************/
/******************************************************/
//This function checks to make sure the user entered appropriate
// format parameters on a distfile read
-void ErrorCheck::validateReadPhil(string command) {
+void ErrorCheck::validateReadPhil() {
try {
ifstream filehandle;
int ableToOpen;
- //checks for valid files
- if (command == "read.list" ) {
- if (listfile == "") { cout << "When executing a read.list you must enter a listfile." << endl; errorFree = false; }
- }else if (command == "read.sabund" ) {
- if (sabundfile == "") { cout << "When executing a read.sabund you must enter a sabundfile." << endl; errorFree = false; }
- }else if (command == "read.rabund" ) {
- if (rabundfile == "") { cout << "When executing a read.rabund you must enter a rabundfile." << endl; errorFree = false; }
+ //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; }
+ }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; }
+ }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; }
+ }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;
}
//checks parameters on the read command
void ErrorCheck::clear() {
//option definitions should go here...
- distfile = "";
+ phylipfile = "";
+ columnfile = "";
listfile = "";
rabundfile = "";
sabundfile = "";
projects / mothur.git / blobdiff