removed validcommands and put its checking in commandfactory.

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index eeaf8ee38ee287691dc8023307f95e098026c9ac..7dd35fd673a7bc62e109a0095efe847d5b097588 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -57,6 +57,48 @@
 CommandFactory::CommandFactory(){
        string s = "";
        command = new NoCommand(s);
+       
+       
+       //initialize list of valid commands
+       commands["read.dist"]                   = "read.dist"; 
+       commands["read.otu"]                    = "read.otu";
+       commands["read.tree"]                   = "read.tree"; 
+       commands["bin.seqs"]                    = "bin.seqs"; 
+       commands["get.oturep"]                  = "get.oturep";
+       commands["cluster"]                             = "cluster"; 
+       commands["unique.seqs"]                 = "unique.seqs"; 
+       commands["dist.seqs"]                   = "dist.seqs";
+       commands["dist.shared"]                 = "dist.shared";
+       commands["collect.single"]              = "collect.single"; 
+       commands["collect.shared"]              = "collect.shared"; 
+       commands["rarefaction.single"]  = "rarefaction.single"; 
+       commands["rarefaction.shared"]  = "rarefaction.shared"; 
+       commands["summary.single"]              = "summary.single"; 
+       commands["summary.shared"]              = "summary.shared"; 
+       commands["parsimony"]                   = "parsimony";
+       commands["unifrac.weighted"]    = "unifrac.weighted"; 
+       commands["unifrac.unweighted"]  = "unifrac.unweighted"; 
+       commands["libshuff"]                    = "libshuff";
+       commands["tree.shared"]                 = "tree.shared";
+       commands["heatmap.bin"]                 = "heatmap.bin";
+       commands["heatmap.sim"]                 = "heatmap.sim";
+       commands["venn"]                                = "venn";
+       commands["get.group"]           = "get.group";
+       commands["get.label"]           = "get.label";
+       commands["get.line"]            = "get.line";
+       commands["get.sabund"]          = "get.sabund";
+       commands["get.rabund"]          = "get.rabund";
+       commands["bootstrap.shared"]    = "bootstrap.shared";
+       commands["concensus"]                   = "concensus";
+       commands["help"]                                = "help"; 
+       commands["filter.seqs"]                 = "filter.seqs";
+       commands["align.seqs"]                  = "align.seqs";
+       commands["summary.seqs"]                = "summary.seqs";
+       commands["screen.seqs"]                 = "screen.seqs";
+       commands["reverse.seqs"]                = "reverse.seqs";
+       commands["trim.seqs"]                   = "trim.seqs";
+       commands["quit"]                                = "quit"; 
+
 }
 /***********************************************************/
 
@@ -126,5 +168,54 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
        }
 
 }
-/***********************************************************/
+
+/***********************************************************************/
+bool CommandFactory::isValidCommand(string command) {
+       try {   
+       
+               //is the command in the map
+               if ((commands.find(command)) != (commands.end())) {
+                       return true;
+               }else{
+                       cout << command << " is not a valid command in Mothur.  Valid commands are ";
+                       for (it = commands.begin(); it != commands.end(); it++) {
+                               cout << it->first << ", ";
+                       }
+                       cout << endl;
+                       return false;
+               }
+               
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the CommandFactory class function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+void CommandFactory::printCommands(ostream& out) {
+       try {   
+               out << "Valid commands are ";
+               for (it = commands.begin(); it != commands.end(); it++) {
+                       out << it->first << ", ";
+               }
+               out << endl;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the CommandFactory class function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+
+