sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 02af6767b00b724459c054839b789798f4b295f7..193c53c4d610111cf369084f1a153400bfbe38e5 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -134,6 +134,13 @@
 #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"
 
 /*******************************************************/
 
@@ -290,7 +297,15 @@ 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";
+    
 
 }
 /***********************************************************/
@@ -503,6 +518,13 @@ 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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -657,6 +679,13 @@ 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                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -797,6 +826,13 @@ 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                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;
@@ -876,6 +912,41 @@ 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);
+       }
+}      
+
+/***********************************************************************/