X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandfactory.cpp;h=387ee10833323300a66a0e6d1161a64bff6fb9ee;hp=02af6767b00b724459c054839b789798f4b295f7;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=2ecee16fec29d4c525f740ec19b27962ca09c050

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 02af676..387ee10 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -134,6 +134,16 @@
 #include "removeotulabelscommand.h"
 #include "makecontigscommand.h"
 #include "loadlogfilecommand.h"
+#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"
 
 /*******************************************************/
 
@@ -290,7 +300,18 @@ CommandFactory::CommandFactory(){
     commands["make.contigs"]        = "make.contigs";
     commands["load.logfile"]        = "load.logfile";
     commands["make.table"]          = "make.table";
+    commands["sff.multiple"]        = "sff.multiple";
 	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";
+    
 
 }
 /***********************************************************/
@@ -503,6 +524,16 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "remove.otulabels")      {	command = new RemoveOtuLabelsCommand(optionString);         }
         else if(commandName == "make.contigs")          {	command = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {	command = new LoadLogfileCommand(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											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -657,6 +688,16 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "remove.otulabels")      {	pipecommand = new RemoveOtuLabelsCommand(optionString);         }
         else if(commandName == "make.contigs")          {	pipecommand = new MakeContigsCommand(optionString);             }
         else if(commandName == "load.logfile")          {	pipecommand = new LoadLogfileCommand(optionString);             }
+        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											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -797,6 +838,16 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "remove.otulabels")      {	shellcommand = new RemoveOtuLabelsCommand();        }
         else if(commandName == "make.contigs")          {	shellcommand = new MakeContigsCommand();            }
         else if(commandName == "load.logfile")          {	shellcommand = new LoadLogfileCommand();            }
+        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											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;
@@ -876,6 +927,41 @@ 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);
+	}
+}      
+
+/***********************************************************************/