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 d813e1b5e22f9184de49151d3183b528c1dfc7cd..b61c2d2dc820c7cf05b7f82d3983017f2d6d4c55 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -127,6 +127,11 @@
 #include "shhhseqscommand.h"
 #include "summaryqualcommand.h"
 #include "otuassociationcommand.h"
+#include "sortseqscommand.h"
+#include "classifytreecommand.h"
+#include "cooccurrencecommand.h"
+#include "pcrseqscommand.h"
+#include "createdatabasecommand.h"
 
 /*******************************************************/
 
@@ -275,6 +280,11 @@ CommandFactory::CommandFactory(){
        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"; 
 
 }
@@ -305,6 +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
@@ -436,6 +447,11 @@ Command* CommandFactory::getCommand(string commandName, string 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;
@@ -581,6 +597,11 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                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;
@@ -714,6 +735,11 @@ Command* CommandFactory::getCommand(string commandName){
                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;
@@ -739,7 +765,7 @@ Command* CommandFactory::getCommand(){
                exit(1);
        }
 }
-/***********************************************************************/
+***********************************************************************/
 bool CommandFactory::isValidCommand(string command) {
        try {