X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=b61c2d2dc820c7cf05b7f82d3983017f2d6d4c55;hb=8da8321bc4d705f6c156248d6229c60a0204f750;hp=2fc6875c6430bd769e3e8b56e484b5da1561a30c;hpb=96f25c3c0f3ba2a1634094de146630dbc9ee0d03;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 2fc6875..b61c2d2 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -123,6 +123,15 @@
 #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"
+#include "cooccurrencecommand.h"
+#include "pcrseqscommand.h"
+#include "createdatabasecommand.h"
 
 /*******************************************************/
 
@@ -201,7 +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";
@@ -241,8 +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";
@@ -258,6 +267,7 @@ CommandFactory::CommandFactory(){
 	commands["chimera.check"]		= "MPIEnabled";
 	commands["chimera.slayer"]		= "MPIEnabled";
 	commands["chimera.uchime"]		= "chimera.uchime";
+	commands["chimera.perseus"]		= "chimera.perseus";
 	commands["chimera.pintail"]		= "MPIEnabled";
 	commands["chimera.bellerophon"]	= "MPIEnabled";
 	commands["screen.seqs"]			= "MPIEnabled";
@@ -266,7 +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"; 
 
 }
@@ -297,6 +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
@@ -424,6 +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;
@@ -565,6 +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;
@@ -694,6 +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;
@@ -719,7 +765,7 @@ Command* CommandFactory::getCommand(){
 		exit(1);
 	}
 }
-/***********************************************************************/
+***********************************************************************/
 bool CommandFactory::isValidCommand(string command) {
 	try {