added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 727f6e821f019ae5c2f7629e1d0afabd33b6e789..aaeec67f1b4eec4e2194fc014e87064c1d5c2b5c 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -65,6 +65,12 @@
 #include "otuhierarchycommand.h"
 #include "setdircommand.h"
 #include "parselistscommand.h"
+#include "parsesffcommand.h"
+#include "chimeraccodecommand.h"
+#include "chimeracheckcommand.h"
+#include "chimeraslayercommand.h"
+#include "chimerapintailcommand.h"
+#include "chimerabellerophoncommand.h"
 
 /*******************************************************/
 
@@ -78,6 +84,12 @@ CommandFactory* CommandFactory::getInstance() {
 /***********************************************************/
 
 /***********************************************************/
+//note: This class is resposible for knowing which commands are mpiEnabled,
+//If a command is not enabled only process 0 will execute the command. 
+//This avoids redundant outputs on pieces of code we have not paralellized. 
+//If you add mpi code to a existing command you need to modify the list below or the code will hang on MPI blocking commands like FIle_open. 
+//example:  commands["dist.seqs"] = "MPIEnabled";
+
 CommandFactory::CommandFactory(){
        string s = "";
        m = MothurOut::getInstance();
@@ -94,7 +106,6 @@ CommandFactory::CommandFactory(){
        commands["get.oturep"]                  = "get.oturep";
        commands["cluster"]                             = "cluster"; 
        commands["unique.seqs"]                 = "unique.seqs"; 
-       commands["dist.seqs"]                   = "MPIEnabled";
        commands["dist.shared"]                 = "dist.shared";
        commands["collect.single"]              = "collect.single"; 
        commands["collect.shared"]              = "collect.shared"; 
@@ -117,13 +128,10 @@ CommandFactory::CommandFactory(){
        commands["bootstrap.shared"]    = "bootstrap.shared";
        //commands["consensus"]                 = "consensus";
        commands["help"]                                = "help"; 
-       commands["filter.seqs"]                 = "MPIEnabled";
-       commands["align.seqs"]                  = "align.seqs";
        commands["summary.seqs"]                = "summary.seqs";
        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";
@@ -131,9 +139,7 @@ CommandFactory::CommandFactory(){
        commands["align.check"]                 = "align.check";
        commands["get.sharedseqs"]              = "get.sharedseqs";
        commands["get.otulist"]                 = "get.otulist";
-       commands["quit"]                                = "MPIEnabled"; 
        commands["hcluster"]                    = "hcluster"; 
-       commands["classify.seqs"]               = "classify.seqs"; 
        commands["phylotype"]                   = "phylotype";
        commands["mgcluster"]                   = "mgcluster";
        commands["pre.cluster"]                 = "pre.cluster";
@@ -142,6 +148,19 @@ CommandFactory::CommandFactory(){
        commands["set.dir"]                             = "set.dir";
        commands["merge.files"]                 = "merge.files";
        commands["parse.list"]                  = "parse.list";
+       commands["parse.sff"]                   = "parse.sff";
+       commands["classify.seqs"]               = "MPIEnabled"; 
+       commands["dist.seqs"]                   = "MPIEnabled";
+       commands["filter.seqs"]                 = "MPIEnabled";
+       commands["align.seqs"]                  = "MPIEnabled";
+       commands["chimera.seqs"]                = "chimera.seqs";
+       commands["chimera.ccode"]               = "MPIEnabled";
+       commands["chimera.check"]               = "MPIEnabled";
+       commands["chimera.slayer"]              = "MPIEnabled";
+       commands["chimera.pintail"]             = "MPIEnabled";
+       commands["chimera.bellerophon"] = "MPIEnabled";
+       commands["quit"]                                = "MPIEnabled"; 
+
 }
 /***********************************************************/
 
@@ -230,6 +249,11 @@ Command* CommandFactory::getCommand(string commandName, string 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 == "chimera.ccode")                 {       command = new ChimeraCcodeCommand(optionString);                        }
+               else if(commandName == "chimera.check")                 {       command = new ChimeraCheckCommand(optionString);                        }
+               else if(commandName == "chimera.slayer")                {       command = new ChimeraSlayerCommand(optionString);                       }
+               else if(commandName == "chimera.pintail")               {       command = new ChimeraPintailCommand(optionString);                      }
+               else if(commandName == "chimera.bellerophon")   {       command = new ChimeraBellerophonCommand(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);                          }
@@ -237,6 +261,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                        }
                else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);                        }
                else if(commandName == "parse.list")                    {       command = new ParseListCommand(optionString);                           }
+               else if(commandName == "parse.sff")                             {       command = new ParseSFFCommand(optionString);                            }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;