//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 ((globaldata->getSharedFile() == "")) { cout << "You must read a groupfile or a sharedfile 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; }
else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
}
- if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
+ if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")){
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 == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")){
+ if (commandName == "get.rabund") {
+ if (globaldata->getListFile() == "") { cout << "You must read a listfile before you can use the get.rabund command." << endl; return false; }
+ }
+
+ if (commandName == "get.sabund") {
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { cout << "You must read a list or rabund before you can use the get.sabund command." << endl; return false; }
+ }
+
+ if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.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, summary.shared, tree.shared, bootstrap.shared or dist.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, bootstrap.shared or dist.shared commands." << endl; return false; }
}
}
+ if (commandName == "tree.shared") {
+ //given no files
+ if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { cout << "You must run the read.otu command or provide a distance file before running the tree.shared command." << endl; return false; }
+ //you want to do single commands
+ else if ((globaldata->getSharedFile() == "") && ((phylipfile != "") || (columnfile != ""))) {
+ validateReadDist();
+ }
+ }
+
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;
errorFree = false;
}
if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; }
+ if (fastafile == "") { cout << "fasta is a required parameter for the get.oturep command." << endl; errorFree = false; }
validateBinFiles();
}
//unable to open
if (ableToOpen == 1) { errorFree = false; }
else { globaldata->inputFileName = sharedfile; }
+ }else if (groupfile != "") {
+ ableToOpen = openInputFile(groupfile, filehandle);
+ filehandle.close();
+ if (ableToOpen == 1) { //unable to open
+ errorFree = false;
+ }
}else{ //no file given
errorFree = false;
}
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; }
+ if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist or a tree.shared command with a distance file you must enter a phylip or a column." << endl; errorFree = false; }
+ else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist or a tree.shared command with a distance file you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
if (columnfile != "") {
if (namefile == "") {
ableToOpen = openInputFile(groupfile, filehandle);
filehandle.close();
if (ableToOpen == 1) { //unable to open
- errorFree = false;;
+ errorFree = false;
}
}
}