X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=41a67297c4199ab819ef7f0498dfd27e6debd515;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=a691509ab0ae00e5f19ae52a8bffe6801fc26a31;hpb=367747fb506bf228d3b2d645868d275ba0714e90;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index a691509..41a6729 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -137,6 +137,17 @@
 #include "sffmultiplecommand.h"
 #include "classifysharedcommand.h"
 #include "filtersharedcommand.h"
+#include "primerdesigncommand.h"
+#include "getdistscommand.h"
+#include "removedistscommand.h"
+#include "mergetaxsummarycommand.h"
+#include "getmetacommunitycommand.h"
+#include "sparcccommand.h"
+#include "makelookupcommand.h"
+#include "renameseqscommand.h"
+#include "makelefsecommand.h"
+#include "lefsecommand.h"
+#include "kruskalwalliscommand.h"
 
 /*******************************************************/
 
@@ -297,6 +308,17 @@ CommandFactory::CommandFactory(){
 	commands["quit"]				= "MPIEnabled"; 
     commands["classify.shared"]		= "classify.shared"; 
     commands["filter.shared"]		= "filter.shared"; 
+    commands["primer.design"]		= "primer.design";
+    commands["get.dists"]           = "get.dists";
+    commands["remove.dists"]        = "remove.dists";
+    commands["merge.taxsummary"]    = "merge.taxsummary";
+    commands["get.metacommunity"]   = "get.metacommunity";
+    commands["sparcc"]              = "sparcc";
+    commands["make.lookup"]         = "make.lookup";
+    commands["rename.seqs"]         = "rename.seqs";
+    commands["make.lefse"]          = "make.lefse";
+    commands["lefse"]               = "lefse";
+    commands["kruskal.wallis"]      = "kruskal.wallis";
     
 
 }
@@ -513,6 +535,17 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "sff.multiple")          {	command = new SffMultipleCommand(optionString);             }
         else if(commandName == "classify.shared")       {	command = new ClassifySharedCommand(optionString);          }
         else if(commandName == "filter.shared")         {	command = new FilterSharedCommand(optionString);            }
+        else if(commandName == "primer.design")         {	command = new PrimerDesignCommand(optionString);            }
+        else if(commandName == "get.dists")             {	command = new GetDistsCommand(optionString);                }
+        else if(commandName == "remove.dists")          {	command = new RemoveDistsCommand(optionString);             }
+        else if(commandName == "merge.taxsummary")      {	command = new MergeTaxSummaryCommand(optionString);         }
+        else if(commandName == "get.metacommunity")     {	command = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "sparcc")                {	command = new SparccCommand(optionString);                  }
+        else if(commandName == "make.lookup")			{	command = new MakeLookupCommand(optionString);				}
+        else if(commandName == "rename.seqs")			{	command = new RenameSeqsCommand(optionString);				}
+        else if(commandName == "make.lefse")			{	command = new MakeLefseCommand(optionString);				}
+        else if(commandName == "lefse")                 {	command = new LefseCommand(optionString);                   }
+        else if(commandName == "kruskal.wallis")        {	command = new KruskalWallisCommand(optionString);           }
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -670,6 +703,17 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "sff.multiple")          {	pipecommand = new SffMultipleCommand(optionString);             }
         else if(commandName == "classify.shared")       {	pipecommand = new ClassifySharedCommand(optionString);          }
         else if(commandName == "filter.shared")         {	pipecommand = new FilterSharedCommand(optionString);            }
+        else if(commandName == "primer.design")         {	pipecommand = new PrimerDesignCommand(optionString);            }
+        else if(commandName == "get.dists")             {	pipecommand = new GetDistsCommand(optionString);                }
+        else if(commandName == "remove.dists")          {	pipecommand = new RemoveDistsCommand(optionString);             }
+        else if(commandName == "merge.taxsummary")      {	pipecommand = new MergeTaxSummaryCommand(optionString);         }
+        else if(commandName == "get.metacommunity")     {	pipecommand = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "sparcc")                {	pipecommand = new SparccCommand(optionString);                  }
+        else if(commandName == "make.lookup")			{	pipecommand = new MakeLookupCommand(optionString);				}
+        else if(commandName == "rename.seqs")			{	pipecommand = new RenameSeqsCommand(optionString);				}
+        else if(commandName == "make.lefse")			{	pipecommand = new MakeLefseCommand(optionString);				}
+        else if(commandName == "lefse")                 {	pipecommand = new LefseCommand(optionString);                   }
+        else if(commandName == "kruskal.wallis")        {	pipecommand = new KruskalWallisCommand(optionString);           }
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -813,6 +857,17 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "sff.multiple")          {	shellcommand = new SffMultipleCommand();            }
         else if(commandName == "classify.shared")       {	shellcommand = new ClassifySharedCommand();         }
         else if(commandName == "filter.shared")         {	shellcommand = new FilterSharedCommand();           }
+        else if(commandName == "primer.design")         {	shellcommand = new PrimerDesignCommand();           }
+        else if(commandName == "get.dists")             {	shellcommand = new GetDistsCommand();               }
+        else if(commandName == "remove.dists")          {	shellcommand = new RemoveDistsCommand();            }
+        else if(commandName == "merge.taxsummary")      {	shellcommand = new MergeTaxSummaryCommand();        }
+        else if(commandName == "get.metacommunity")     {	shellcommand = new GetMetaCommunityCommand();       }
+        else if(commandName == "sparcc")                {	shellcommand = new SparccCommand();                 }
+        else if(commandName == "make.lookup")			{	shellcommand = new MakeLookupCommand();				}
+        else if(commandName == "rename.seqs")			{	shellcommand = new RenameSeqsCommand();				}
+        else if(commandName == "make.lefse")			{	shellcommand = new MakeLefseCommand();				}
+        else if(commandName == "lefse")                 {	shellcommand = new LefseCommand();                  }
+        else if(commandName == "kruskal.wallis")        {	shellcommand = new KruskalWallisCommand();          }
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;
@@ -892,6 +947,41 @@ void CommandFactory::printCommands(ostream& out) {
 	}
 }
 /***********************************************************************/
+void CommandFactory::printCommandsCategories(ostream& out) {
+    try {
+        map<string, string> commands = getListCommands();
+        map<string, string>::iterator it;
+
+        map<string, string> categories;
+        map<string, string>::iterator itCat;
+        //loop through each command outputting info
+        for (it = commands.begin(); it != commands.end(); it++) {
+    
+            Command* thisCommand = getCommand(it->first);
+    
+            //don't add hidden commands
+            if (thisCommand->getCommandCategory() != "Hidden") {
+                itCat = categories.find(thisCommand->getCommandCategory());
+                if (itCat == categories.end()) {
+                    categories[thisCommand->getCommandCategory()] = thisCommand->getCommandName();
+                }else {
+                    categories[thisCommand->getCommandCategory()] += ", " + thisCommand->getCommandName();
+                }
+            }
+        }
+        
+        for (itCat = categories.begin(); itCat != categories.end(); itCat++) {
+            out << itCat->first << " commmands include: " << itCat->second << endl;
+        }
+
+    }
+	catch(exception& e) {
+		m->errorOut(e, "CommandFactory", "printCommandsCategories");
+		exit(1);
+	}
+}      
+
+/***********************************************************************/