added sorted parameter to get.oturep, added error checking to chimera classes in...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index db11f8c0dc890dff846787dee0fc48ea8930384a..c33de86f5c5a97fe9599a8871b190194170e1a6c 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -12,7 +12,6 @@
 #include "readtreecommand.h"
 #include "readotucommand.h"
 #include "clustercommand.h"
-#include "parselistcommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
 #include "getgroupcommand.h"
@@ -39,7 +38,7 @@
 #include "getoturepcommand.h"
 #include "treegroupscommand.h"
 #include "bootstrapsharedcommand.h"
-#include "concensuscommand.h"
+//#include "consensuscommand.h"
 #include "distancecommand.h"
 #include "aligncommand.h"
 #include "matrixoutputcommand.h"
@@ -50,11 +49,32 @@
 #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"
 
+/*******************************************************/
+
+/******************************************************/
+CommandFactory* CommandFactory::getInstance() {
+       if( _uniqueInstance == 0) {
+               _uniqueInstance = new CommandFactory();
+       }
+       return _uniqueInstance;
+}
 /***********************************************************/
 
 /***********************************************************/
 CommandFactory::CommandFactory(){
+       _uniqueInstance = 0;
        string s = "";
        command = new NoCommand(s);
        
@@ -89,7 +109,7 @@ CommandFactory::CommandFactory(){
        commands["get.sabund"]          = "get.sabund";
        commands["get.rabund"]          = "get.rabund";
        commands["bootstrap.shared"]    = "bootstrap.shared";
-       commands["concensus"]                   = "concensus";
+       //commands["consensus"]                 = "consensus";
        commands["help"]                                = "help"; 
        commands["filter.seqs"]                 = "filter.seqs";
        commands["align.seqs"]                  = "align.seqs";
@@ -97,7 +117,18 @@ 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";
 
 }
 /***********************************************************/
@@ -146,14 +177,25 @@ 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 == "concensus")                             {   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                                                                                    {       command = new NoCommand(optionString);                                  }
 
                return command;
@@ -163,7 +205,22 @@ 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 {