fixed some bugs found while testing 1.8

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 2783aa3acfe56a38d2479af5696e542f2228693b..5eb4ff5df0eaf4999808925e658e61c1eedccf31 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"
@@ -52,7 +51,29 @@
 #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"
+#include "otuhierarchycommand.h"
+#include "setdircommand.h"
 
+/*******************************************************/
+
+/******************************************************/
+CommandFactory* CommandFactory::getInstance() {
+       if( _uniqueInstance == 0) {
+               _uniqueInstance = new CommandFactory();
+       }
+       return _uniqueInstance;
+}
 /***********************************************************/
 
 /***********************************************************/
@@ -60,6 +81,7 @@ CommandFactory::CommandFactory(){
        string s = "";
        command = new NoCommand(s);
        
+       outputDir = ""; inputDir = "";
        
        //initialize list of valid commands
        commands["read.dist"]                   = "read.dist"; 
@@ -87,7 +109,6 @@ 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";
@@ -102,13 +123,26 @@ CommandFactory::CommandFactory(){
        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";
+       commands["otu.hierarchy"]               = "otu.hierarchy";
+       commands["set.dir"]                             = "set.dir";
 }
 /***********************************************************/
 
 /***********************************************************/
 CommandFactory::~CommandFactory(){
+       _uniqueInstance = 0;
        delete command;
 }
 
@@ -119,7 +153,19 @@ 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);                    }
@@ -138,7 +184,6 @@ 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);                        }
@@ -161,7 +206,20 @@ Command* CommandFactory::getCommand(string commandName, string 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 if(commandName == "otu.hierarchy")                 {       command = new OtuHierarchyCommand(optionString);                }
+               else if(commandName == "set.dir")                               {       command = new SetDirectoryCommand(optionString);        }
                else                                                                                    {       command = new NoCommand(optionString);                                  }
 
                return command;
@@ -171,7 +229,22 @@ 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 {