/******************************************************/
void ErrorCheck::refresh() {
- 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();
- randomtree = globaldata->getRandomTree();
- sharedfile = globaldata->getSharedFile();
+ //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();
+ //randomtree = globaldata->getRandomTree();
+ //sharedfile = globaldata->getSharedFile();
}
/*******************************************************/
/******************************************************/
-ErrorCheck::~ErrorCheck() {}
+ErrorCheck::~ErrorCheck() {
+ delete validCommand;
+ delete validParameter;
+}
/*******************************************************/
if (validCommand->isValidCommand(commandName) != true) { return false; }
string parameter, value;
+
//reads in parameters and values
if((optionText != "") && (commandName != "help")){
while((optionText.find_first_of(',') != -1) && (errorFree)) { //while there are parameters
splitAtEquals(parameter, value);
//is it a valid parameter
- if (validParameter->isValidParameter(parameter) != true) { return false; }
+ if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
if (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
if (parameter == "fileroot" ) { fileroot = value; }
if (parameter == "line" ) { line = value; }
if (parameter == "label" ) { label = value; }
+ if (parameter == "abund" ) { abund = value; }
if (parameter == "random" ) { randomtree = value; }
-
+ if (parameter == "sorted" ) { sorted = value; }
+ if (parameter == "scale" ) { scale = value; }
+
}
//gets the last parameter and value
value = optionText;
splitAtEquals(parameter, value);
//is it a valid parameter
- if (validParameter->isValidParameter(parameter) != true) { return false; }
+ if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
+
if (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
if (parameter == "line" ) { line = value; }
if (parameter == "label" ) { label = value; }
if (parameter == "random" ) { randomtree = value; }
-
+ if (parameter == "abund" ) { abund = value; }
+ if (parameter == "sorted" ) { sorted = value; }
+ if (parameter == "scale" ) { scale = 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; }
+ //check for valid files
if (commandName == "read.dist") {
validateReadFiles();
validateReadDist();
//you want to do shared commands
if ((listfile != "") && (groupfile != "")) {
validateParseFiles(); //checks the listfile and groupfile parameters
- }else { //you want to do single commands
+ //you want to do single commands
+ }else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){
validateReadFiles();
validateReadPhil();
+ //you have not given a file
+ }else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
+ cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false;
+ //you want to do shared commands with a shared file
+ }else if (sharedfile != "") {//you are reading a shared file
+ validateReadFiles();
}
- }else if (commandName == "read.shared") {
- //you want to do shared commands with just the shared file
- validateReadFiles();
}else if (commandName == "read.tree") {
validateTreeFiles(); //checks the treefile and groupfile parameters
}else if (commandName == "deconvolute") {
}
//are you trying to cluster before you have read something
- if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
- (commandName == "cluster") && (globaldata->getListVector() == NULL)) {
+ if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
+ ((commandName == "cluster") && (globaldata->gListVector == NULL))) {
cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
errorFree = false;
}
+ if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
+ cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false;
+ }
+
if (commandName == "parsimony") {
//are you trying to use parsimony without reading a tree or saying you want random distribution
if (randomtree == "") {
}
//check for valid method
+ if(commandName == "get.group") {
+ if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
+ }
+ if (commandName == "get.label" || commandName == "get.line") {
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.label or get.line command." << endl; return false; }
+ }
if (commandName == "cluster") {
if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << 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") ){
+ if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "tree.shared") || (commandName == "bootstrap.shared")){
if (globaldata->getSharedFile() == "") {
- if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared 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, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
+ if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared, summary.shared, tree.shared or bootstrap.shared commands." << endl; return false; }
+ else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared, summary.shared, tree.shared or bootstrap.shared commands." << endl; return false; }
}
}
-
+
+ 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 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;
}
//unable to open
if (ableToOpen == 1) { errorFree = false; }
else { globaldata->inputFileName = phylipfile; }
- //are we reading a phylipfile
+ //are we reading a columnfile
}else if (columnfile != "") {
ableToOpen = openInputFile(columnfile, filehandle);
filehandle.close();
ifstream filehandle;
int ableToOpen;
+ if (groupfile != "") {
+ ableToOpen = openInputFile(groupfile, filehandle);
+ filehandle.close();
+ //unable to open
+ if (ableToOpen == 1) { 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; }
}else if (sabundfile != "") {
if ((listfile != "") || (rabundfile != "")) {
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 == "")) {
+ }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) {
cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
}
}
/*******************************************************/
+/******************************************************/
+//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() {
projects / mothur.git / blobdiff