added create.database command. fixed help in get.sharedseqs. added new constructor...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 69bb568e761f590e2419ee61079783679c914efa..b61c2d2dc820c7cf05b7f82d3983017f2d6d4c55 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -124,6 +124,14 @@
 #include "clearmemorycommand.h"
 #include "summarytaxcommand.h"
 #include "chimeraperseuscommand.h"
+#include "shhhseqscommand.h"
+#include "summaryqualcommand.h"
+#include "otuassociationcommand.h"
+#include "sortseqscommand.h"
+#include "classifytreecommand.h"
+#include "cooccurrencecommand.h"
+#include "pcrseqscommand.h"
+#include "createdatabasecommand.h"
 
 /*******************************************************/
 
@@ -202,7 +210,7 @@ CommandFactory::CommandFactory(){
        commands["pre.cluster"]                 = "pre.cluster";
        commands["pcoa"]                                = "pcoa";
        commands["otu.hierarchy"]               = "otu.hierarchy";
-       commands["set.dir"]                             = "set.dir";
+       commands["set.dir"]                             = "MPIEnabled";
        commands["merge.files"]                 = "merge.files";
        commands["parse.list"]                  = "parse.list";
        commands["set.logfile"]                 = "set.logfile";
@@ -242,8 +250,8 @@ CommandFactory::CommandFactory(){
        commands["anosim"]                              = "anosim";
        commands["make.fastq"]                  = "make.fastq";
        commands["merge.groups"]                = "merge.groups";
-       commands["get.current"]                 = "get.current";
-       commands["set.current"]                 = "set.current";
+       commands["get.current"]                 = "MPIEnabled";
+       commands["set.current"]                 = "MPIEnabled";
        commands["get.commandinfo"]             = "get.commandinfo";
        commands["deunique.tree"]               = "deunique.tree";
        commands["count.seqs"]                  = "count.seqs";
@@ -268,8 +276,15 @@ CommandFactory::CommandFactory(){
        commands["shhh.flows"]                  = "MPIEnabled";
        commands["sens.spec"]                   = "sens.spec";
        commands["seq.error"]                   = "seq.error";
-       commands["seq.error"]                   = "summary.tax";
-       
+       commands["summary.tax"]                 = "summary.tax";
+       commands["summary.qual"]                = "summary.qual";
+       commands["shhh.seqs"]                   = "shhh.seqs";
+       commands["otu.association"]             = "otu.association";
+    commands["sort.seqs"]           = "sort.seqs";
+    commands["classify.tree"]       = "classify.tree";
+    commands["cooccurrence"]        = "cooccurrence";
+    commands["pcr.seqs"]            = "pcr.seqs";
+    commands["create.database"]     = "create.database";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -300,6 +315,7 @@ CommandFactory::~CommandFactory(){
 //This function calls the appropriate command fucntions based on user input.
 Command* CommandFactory::getCommand(string commandName, string optionString){
        try {
+        
                delete command;   //delete the old command
                
                //user has opted to redirect output from dir where input files are located to some other place
@@ -427,7 +443,15 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "count.groups")                  {       command = new CountGroupsCommand(optionString);                         }
                else if(commandName == "clear.memory")                  {       command = new ClearMemoryCommand(optionString);                         }
                else if(commandName == "summary.tax")                   {       command = new SummaryTaxCommand(optionString);                          }
+               else if(commandName == "summary.qual")                  {       command = new SummaryQualCommand(optionString);                         }
                else if(commandName == "chimera.perseus")               {       command = new ChimeraPerseusCommand(optionString);                      }
+               else if(commandName == "shhh.seqs")                             {       command = new ShhhSeqsCommand(optionString);                            }
+               else if(commandName == "otu.association")               {       command = new OTUAssociationCommand(optionString);                      }
+        else if(commandName == "sort.seqs")             {      command = new SortSeqsCommand(optionString);                }
+        else if(commandName == "classify.tree")         {      command = new ClassifyTreeCommand(optionString);            }
+        else if(commandName == "cooccurrence")          {      command = new CooccurrenceCommand(optionString);            }
+        else if(commandName == "pcr.seqs")              {      command = new PcrSeqsCommand(optionString);                 }
+        else if(commandName == "create.database")       {      command = new CreateDatabaseCommand(optionString);          }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -569,7 +593,15 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "count.groups")                  {       pipecommand = new CountGroupsCommand(optionString);                             }
                else if(commandName == "clear.memory")                  {       pipecommand = new ClearMemoryCommand(optionString);                             }
                else if(commandName == "summary.tax")                   {       pipecommand = new SummaryTaxCommand(optionString);                              }
+               else if(commandName == "summary.qual")                  {       pipecommand = new SummaryQualCommand(optionString);                             }
                else if(commandName == "chimera.perseus")               {       pipecommand = new ChimeraPerseusCommand(optionString);                  }
+               else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhhSeqsCommand(optionString);                                }
+               else if(commandName == "otu.association")               {       pipecommand = new OTUAssociationCommand(optionString);                  }
+        else if(commandName == "sort.seqs")             {      pipecommand = new SortSeqsCommand(optionString);                }
+        else if(commandName == "classify.tree")         {      pipecommand = new ClassifyTreeCommand(optionString);            }
+        else if(commandName == "cooccurrence")          {      pipecommand = new CooccurrenceCommand(optionString);            }
+        else if(commandName == "pcr.seqs")              {      pipecommand = new PcrSeqsCommand(optionString);                 }
+        else if(commandName == "create.database")       {      pipecommand = new CreateDatabaseCommand(optionString);          }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -699,7 +731,15 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "count.groups")                  {       shellcommand = new CountGroupsCommand();                        }
                else if(commandName == "clear.memory")                  {       shellcommand = new ClearMemoryCommand();                        }
                else if(commandName == "summary.tax")                   {       shellcommand = new SummaryTaxCommand();                         }
+               else if(commandName == "summary.qual")                  {       shellcommand = new SummaryQualCommand();                        }
                else if(commandName == "chimera.perseus")               {       shellcommand = new ChimeraPerseusCommand();                     }
+               else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhhSeqsCommand();                           }
+               else if(commandName == "otu.association")               {       shellcommand = new OTUAssociationCommand();                     }
+        else if(commandName == "sort.seqs")             {      shellcommand = new SortSeqsCommand();               }
+        else if(commandName == "classify.tree")         {      shellcommand = new ClassifyTreeCommand();           }
+        else if(commandName == "cooccurrence")          {      shellcommand = new CooccurrenceCommand();           }
+        else if(commandName == "pcr.seqs")              {      shellcommand = new PcrSeqsCommand();                }
+        else if(commandName == "create.database")       {      shellcommand = new CreateDatabaseCommand();         }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;
@@ -725,7 +765,7 @@ Command* CommandFactory::getCommand(){
                exit(1);
        }
 }
-/***********************************************************************/
+***********************************************************************/
 bool CommandFactory::isValidCommand(string command) {
        try {