added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 364c5ed2eae3f9cb90dc4db6d3edced157c2168d..579abe82cd4019ab265dcce4220d58aea6924e67 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -125,6 +125,12 @@
 #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"
 
 /*******************************************************/
 
@@ -203,7 +209,7 @@ 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";
@@ -243,8 +249,8 @@ 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";
@@ -270,8 +276,13 @@ CommandFactory::CommandFactory(){
        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["cooccurrence"]        = "cooccurrence";
+    commands["pcr.seqs"]            = "pcr.seqs";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -429,8 +440,14 @@ 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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -572,8 +589,14 @@ 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                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -703,8 +726,14 @@ 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                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;
@@ -730,7 +759,7 @@ Command* CommandFactory::getCommand(){
                exit(1);
        }
 }
-/***********************************************************************/
+***********************************************************************/
 bool CommandFactory::isValidCommand(string command) {
        try {