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) != 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 == "randomtree" ) { randomtree = value; }
-
+ if (parameter == "abund" ) { abund = value; }
+ if (parameter == "random" ) { randomtree = 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) != 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 == "randomtree" ) { randomtree = value; }
-
+ if (parameter == "random" ) { randomtree = value; }
+ if (parameter == "abund" ) { abund = 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; }
- //make sure you have a valid random tree value
- if ((randomtree != "0") && (randomtree != "1")) { cout << randomtree << " is not a valid randomtree value. Valid values for randomtree are 0, (meaning you have read your own trees) or 1 (meaning you want to random distribution of trees)." << endl; return false; }
-
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
+ }else if (listfile != "") { //you want to do single commands
validateReadFiles();
validateReadPhil();
+ }else if ((listfile == "") && (sharedfile == "")) {
+ cout << "You must enter either a listfile or a sharedfile with the read.otu command. " << endl; return false;
+ }else{//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)) {
+ cout << "You must read in a matrix 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 == "0") {
+ if (randomtree == "") {
if (globaldata->gTree.size() == 0) {
- cout << "You must read a treefile and a groupfile or set the randomtree parameter to 1, before you may execute the parsimony command." << endl; return false; }
+ cout << "You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command." << endl; return false; }
}
}
}
//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; }
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; }
}
}
-
+
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; }
projects / mothur.git / blobdiff