removed unused copy constructors and comments within comments that where causing...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 5aaa7b7b120ffdd5b0258b16643ce4bad89be93e..303bf084c15b6d2f525ed70152348374b00f03b0 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -120,7 +120,15 @@
 #include "getcommandinfocommand.h"
 #include "deuniquetreecommand.h"
 #include "countseqscommand.h"
+#include "countgroupscommand.h"
 #include "clearmemorycommand.h"
+#include "summarytaxcommand.h"
+#include "chimeraperseuscommand.h"
+#include "shhhseqscommand.h"
+#include "summaryqualcommand.h"
+#include "otuassociationcommand.h"
+#include "sortseqscommand.h"
+#include "classifytreecommand.h"
 
 /*******************************************************/
 
@@ -199,7 +207,7 @@ 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";
@@ -239,11 +247,12 @@ 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";
+       commands["count.groups"]                = "count.groups";
        commands["clear.memory"]                = "clear.memory";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
@@ -254,15 +263,22 @@ CommandFactory::CommandFactory(){
        commands["chimera.ccode"]               = "MPIEnabled";
        commands["chimera.check"]               = "MPIEnabled";
        commands["chimera.slayer"]              = "MPIEnabled";
-       commands["chimera.uchime"]              = "MPIEnabled";
+       commands["chimera.uchime"]              = "chimera.uchime";
+       commands["chimera.perseus"]             = "chimera.perseus";
        commands["chimera.pintail"]             = "MPIEnabled";
        commands["chimera.bellerophon"] = "MPIEnabled";
        commands["screen.seqs"]                 = "MPIEnabled";
        commands["summary.seqs"]                = "MPIEnabled";
        commands["cluster.split"]               = "MPIEnabled";
-       commands["shhh.seqs"]                   = "MPIEnabled";
+       commands["shhh.flows"]                  = "MPIEnabled";
        commands["sens.spec"]                   = "sens.spec";
        commands["seq.error"]                   = "seq.error";
+       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["quit"]                                = "MPIEnabled"; 
 
 }
@@ -345,7 +361,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                         }
                else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                            }
                else if(commandName == "trim.flows")                    {       command = new TrimFlowsCommand(optionString);                           }
-               else if(commandName == "shhh.seqs")                             {       command = new ShhherCommand(optionString);                                      }
+               else if(commandName == "shhh.flows")                    {       command = new ShhherCommand(optionString);                                      }
                else if(commandName == "list.seqs")                             {       command = new ListSeqsCommand(optionString);                            }
                else if(commandName == "get.seqs")                              {       command = new GetSeqsCommand(optionString);                                     }
                else if(commandName == "remove.seqs")                   {       command = new RemoveSeqsCommand(optionString);                          }
@@ -417,7 +433,15 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "get.commandinfo")               {       command = new GetCommandInfoCommand(optionString);                      }
                else if(commandName == "deunique.tree")                 {       command = new DeuniqueTreeCommand(optionString);                        }
                else if(commandName == "count.seqs")                    {       command = new CountSeqsCommand(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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -485,7 +509,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "reverse.seqs")                  {       pipecommand = new ReverseSeqsCommand(optionString);                             }
                else if(commandName == "trim.seqs")                             {       pipecommand = new TrimSeqsCommand(optionString);                                }
                else if(commandName == "trim.flows")                    {       pipecommand = new TrimFlowsCommand(optionString);                               }
-               else if(commandName == "shhh.seqs")                             {       pipecommand = new ShhherCommand(optionString);                                  }
+               else if(commandName == "shhh.flows")                    {       pipecommand = new ShhherCommand(optionString);                                  }
                else if(commandName == "list.seqs")                             {       pipecommand = new ListSeqsCommand(optionString);                                }
                else if(commandName == "get.seqs")                              {       pipecommand = new GetSeqsCommand(optionString);                                 }
                else if(commandName == "remove.seqs")                   {       pipecommand = new RemoveSeqsCommand(optionString);                              }
@@ -556,7 +580,15 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "get.commandinfo")               {       pipecommand = new GetCommandInfoCommand(optionString);                  }
                else if(commandName == "deunique.tree")                 {       pipecommand = new DeuniqueTreeCommand(optionString);                    }
                else if(commandName == "count.seqs")                    {       pipecommand = new CountSeqsCommand(optionString);                               }
+               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                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -612,7 +644,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "reverse.seqs")                  {       shellcommand = new ReverseSeqsCommand();                        }
                else if(commandName == "trim.seqs")                             {       shellcommand = new TrimSeqsCommand();                           }
                else if(commandName == "trim.flows")                    {       shellcommand = new TrimFlowsCommand();                          }
-               else if(commandName == "shhh.seqs")                             {       shellcommand = new ShhherCommand();                                     }
+               else if(commandName == "shhh.flows")                    {       shellcommand = new ShhherCommand();                                     }
                else if(commandName == "list.seqs")                             {       shellcommand = new ListSeqsCommand();                           }
                else if(commandName == "get.seqs")                              {       shellcommand = new GetSeqsCommand();                            }
                else if(commandName == "remove.seqs")                   {       shellcommand = new RemoveSeqsCommand();                         }
@@ -683,7 +715,15 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "get.commandinfo")               {       shellcommand = new GetCommandInfoCommand();                     }
                else if(commandName == "deunique.tree")                 {       shellcommand = new DeuniqueTreeCommand();                       }
                else if(commandName == "count.seqs")                    {       shellcommand = new CountSeqsCommand();                          }
+               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                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;
@@ -709,7 +749,7 @@ Command* CommandFactory::getCommand(){
                exit(1);
        }
 }
-/***********************************************************************/
+***********************************************************************/
 bool CommandFactory::isValidCommand(string command) {
        try {