#include "collectsharedcommand.h"
#include "getgroupcommand.h"
#include "getlabelcommand.h"
-#include "getlinecommand.h"
#include "rarefactcommand.h"
#include "summarycommand.h"
#include "summarysharedcommand.h"
#include "phylotypecommand.h"
#include "mgclustercommand.h"
#include "preclustercommand.h"
+#include "pcacommand.h"
+#include "otuhierarchycommand.h"
+#include "setdircommand.h"
/*******************************************************/
/***********************************************************/
CommandFactory::CommandFactory(){
- _uniqueInstance = 0;
string s = "";
command = new NoCommand(s);
+ outputDir = ""; inputDir = "";
//initialize list of valid commands
commands["read.dist"] = "read.dist";
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";
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";
}
/***********************************************************/
/***********************************************************/
CommandFactory::~CommandFactory(){
+ _uniqueInstance = 0;
delete command;
}
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); }
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); }
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 { command = new NoCommand(optionString); }
return command;