added pca command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 43f6769f92de125e9b76074e2a2d91cdb9ca3889..2417d8dda900fe4aac1cdf0d4ebea36209c2796c 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -49,11 +49,35 @@
 #include "reversecommand.h"
 #include "trimseqscommand.h"
 #include "mergefilecommand.h"
+#include "chimeraseqscommand.h"
+#include "listseqscommand.h"
+#include "getseqscommand.h"
+#include "removeseqscommand.h"
+#include "systemcommand.h"
+#include "secondarystructurecommand.h"
+#include "getsharedotucommand.h"
+#include "getlistcountcommand.h"
+#include "hclustercommand.h"
+#include "classifyseqscommand.h"
+#include "phylotypecommand.h"
+#include "mgclustercommand.h"
+#include "preclustercommand.h"
+#include "pcacommand.h"
 
+/*******************************************************/
+
+/******************************************************/
+CommandFactory* CommandFactory::getInstance() {
+       if( _uniqueInstance == 0) {
+               _uniqueInstance = new CommandFactory();
+       }
+       return _uniqueInstance;
+}
 /***********************************************************/
 
 /***********************************************************/
 CommandFactory::CommandFactory(){
+       _uniqueInstance = 0;
        string s = "";
        command = new NoCommand(s);
        
@@ -96,7 +120,21 @@ CommandFactory::CommandFactory(){
        commands["screen.seqs"]                 = "screen.seqs";
        commands["reverse.seqs"]                = "reverse.seqs";
        commands["trim.seqs"]                   = "trim.seqs";
+       commands["chimera.seqs"]                = "chimera.seqs";
+       commands["list.seqs"]                   = "list.seqs";
+       commands["get.seqs"]                    = "get.seqs";
+       commands["remove.seqs"]                 = "get.seqs";
+       commands["system"]                              = "system";
+       commands["align.check"]                 = "align.check";
+       commands["get.sharedseqs"]              = "get.sharedseqs";
+       commands["get.otulist"]                 = "get.otulist";
        commands["quit"]                                = "quit"; 
+       commands["hcluster"]                    = "hcluster"; 
+       commands["classify.seqs"]               = "classify.seqs"; 
+       commands["phylotype"]                   = "phylotype";
+       commands["mgcluster"]                   = "mgcluster";
+       commands["pre.cluster"]                 = "pre.cluster";
+       commands["pca"]                                 = "pca";
 
 }
 /***********************************************************/
@@ -145,14 +183,28 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "tree.shared")                   {   command = new TreeGroupCommand(optionString);                       }
                else if(commandName == "dist.shared")                   {   command = new MatrixOutputCommand(optionString);            }
                else if(commandName == "bootstrap.shared")              {   command = new BootSharedCommand(optionString);                      }
-               //else if(commandName == "consensus")                           {   command = new ConcensusCommand(optionString);                       }
+               //else if(commandName == "consensus")                   {   command = new ConcensusCommand(optionString);                       }
                else if(commandName == "dist.seqs")                             {   command = new DistanceCommand(optionString);                        }
                else if(commandName == "align.seqs")                    {   command = new AlignCommand(optionString);                           }
                else if(commandName == "summary.seqs")                  {       command = new SeqSummaryCommand(optionString);                  }
                else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                  }
                else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                 }
                else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(optionString);                    }
+               else if(commandName == "chimera.seqs")                  {       command = new ChimeraSeqsCommand(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);                  }
                else if(commandName == "merge.files")                   {       command = new MergeFileCommand(optionString);                   }
+               else if(commandName == "system")                                {       command = new SystemCommand(optionString);                              }
+               else if(commandName == "align.check")                   {       command = new AlignCheckCommand(optionString);                  }
+               else if(commandName == "get.sharedseqs")                {       command = new GetSharedOTUCommand(optionString);                }
+               else if(commandName == "get.otulist")                   {       command = new GetListCountCommand(optionString);                }
+               else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                    }
+               else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                }
+               else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                   }
+               else if(commandName == "mgcluster")                             {       command = new MGClusterCommand(optionString);                   }
+               else if(commandName == "pre.cluster")                   {       command = new PreClusterCommand(optionString);                  }
+               else if(commandName == "pca")                                   {       command = new PCACommand(optionString);                                 }
                else                                                                                    {       command = new NoCommand(optionString);                                  }
 
                return command;
@@ -162,7 +214,22 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                exit(1);
        }
 }
+/***********************************************************/
+//This function is used to interrupt a command
+Command* CommandFactory::getCommand(){
+       try {
+               delete command;   //delete the old command
 
+               string s = "";
+           command = new NoCommand(s);
+       
+               return command;
+       }
+       catch(exception& e) {
+               errorOut(e, "CommandFactory", "getCommand");
+               exit(1);
+       }
+}
 /***********************************************************************/
 bool CommandFactory::isValidCommand(string command) {
        try {