added parse.list command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index d2b22d59b06c469a12c7fce92b132a7971453f50..baef2164942f5e637f43d8b3b6431091ef13ca63 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -16,7 +16,6 @@
 #include "collectsharedcommand.h"
 #include "getgroupcommand.h"
 #include "getlabelcommand.h"
-#include "getlinecommand.h"
 #include "rarefactcommand.h"
 #include "summarycommand.h"
 #include "summarysharedcommand.h"
@@ -62,6 +61,10 @@
 #include "phylotypecommand.h"
 #include "mgclustercommand.h"
 #include "preclustercommand.h"
+#include "pcacommand.h"
+#include "otuhierarchycommand.h"
+#include "setdircommand.h"
+#include "parselistscommand.h"
 
 /*******************************************************/
 
@@ -76,10 +79,10 @@ CommandFactory* CommandFactory::getInstance() {
 
 /***********************************************************/
 CommandFactory::CommandFactory(){
-       _uniqueInstance = 0;
        string s = "";
        command = new NoCommand(s);
        
+       outputDir = ""; inputDir = "";
        
        //initialize list of valid commands
        commands["read.dist"]                   = "read.dist"; 
@@ -107,7 +110,6 @@ CommandFactory::CommandFactory(){
        commands["venn"]                                = "venn";
        commands["get.group"]           = "get.group";
        commands["get.label"]           = "get.label";
-       commands["get.line"]            = "get.line";
        commands["get.sabund"]          = "get.sabund";
        commands["get.rabund"]          = "get.rabund";
        commands["bootstrap.shared"]    = "bootstrap.shared";
@@ -133,12 +135,17 @@ CommandFactory::CommandFactory(){
        commands["phylotype"]                   = "phylotype";
        commands["mgcluster"]                   = "mgcluster";
        commands["pre.cluster"]                 = "pre.cluster";
-
+       commands["pcoa"]                                = "pcoa";
+       commands["otu.hierarchy"]               = "otu.hierarchy";
+       commands["set.dir"]                             = "set.dir";
+       commands["merge.files"]                 = "merge.files";
+       commands["parse.list"]                  = "parse.list";
 }
 /***********************************************************/
 
 /***********************************************************/
 CommandFactory::~CommandFactory(){
+       _uniqueInstance = 0;
        delete command;
 }
 
@@ -149,7 +156,19 @@ CommandFactory::~CommandFactory(){
 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
+               if (outputDir != "") { 
+                       if (optionString != "") { optionString += ", outputdir=" + outputDir; }
+                       else { optionString += "outputdir=" + outputDir; }
+               }
+               
+               //user has opted to redirect input from dir where mothur.exe is located to some other place
+               if (inputDir != "") { 
+                       if (optionString != "") { optionString += ", inputdir=" + inputDir; }
+                       else { optionString += "inputdir=" + inputDir; }
+               }
+               
                if(commandName == "read.dist")                                  {       command = new ReadDistCommand(optionString);                    }
                else if(commandName == "read.otu")                              {       command = new ReadOtuCommand(optionString);                             }
                else if(commandName == "read.tree")                             {       command = new ReadTreeCommand(optionString);                    }
@@ -168,7 +187,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "unifrac.unweighted")    {       command = new UnifracUnweightedCommand(optionString);   }
                else if(commandName == "get.group")             {   command = new GetgroupCommand(optionString);                        }
                else if(commandName == "get.label")             {   command = new GetlabelCommand(optionString);                        }
-               else if(commandName == "get.line")              {   command = new GetlineCommand(optionString);                         }
                else if(commandName == "get.sabund")            {   command = new GetSAbundCommand(optionString);                       }
                else if(commandName == "get.rabund")            {   command = new GetRAbundCommand(optionString);                       }
                else if(commandName == "libshuff")              {   command = new LibShuffCommand(optionString);                        }
@@ -202,6 +220,10 @@ Command* CommandFactory::getCommand(string commandName, string 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 == "pcoa")                                  {       command = new PCACommand(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                                                                                    {       command = new NoCommand(optionString);                                  }
 
                return command;