X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=b61c2d2dc820c7cf05b7f82d3983017f2d6d4c55;hb=8da8321bc4d705f6c156248d6229c60a0204f750;hp=bdcfbbab528a785abce1330a3bb6b19d8212fdd6;hpb=597560b3c23f03d0069082cf096ce65e0c087519;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index bdcfbba..b61c2d2 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -130,6 +130,8 @@
 #include "sortseqscommand.h"
 #include "classifytreecommand.h"
 #include "cooccurrencecommand.h"
+#include "pcrseqscommand.h"
+#include "createdatabasecommand.h"
 
 /*******************************************************/
 
@@ -281,6 +283,8 @@ CommandFactory::CommandFactory(){
     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"; 
 
 }
@@ -311,6 +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
@@ -445,6 +450,8 @@ Command* CommandFactory::getCommand(string commandName, string 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;
@@ -593,6 +600,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         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;
@@ -729,6 +738,8 @@ Command* CommandFactory::getCommand(string commandName){
         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;