X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=2822d0b9920a0f5cc5005cf01ce653b38b9ede6d;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=d813e1b5e22f9184de49151d3183b528c1dfc7cd;hpb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;p=mothur.git

diff --git a/commandfactory.cpp b/commandfactory.cpp
index d813e1b..2822d0b 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -36,8 +36,6 @@
 #include "binsequencecommand.h"
 #include "getoturepcommand.h"
 #include "treegroupscommand.h"
-#include "bootstrapsharedcommand.h"
-//#include "consensuscommand.h"
 #include "distancecommand.h"
 #include "aligncommand.h"
 #include "matrixoutputcommand.h"
@@ -127,6 +125,17 @@
 #include "shhhseqscommand.h"
 #include "summaryqualcommand.h"
 #include "otuassociationcommand.h"
+#include "sortseqscommand.h"
+#include "classifytreecommand.h"
+#include "cooccurrencecommand.h"
+#include "pcrseqscommand.h"
+#include "createdatabasecommand.h"
+#include "makebiomcommand.h"
+#include "getcoremicrobiomecommand.h"
+#include "listotulabelscommand.h"
+#include "getotulabelscommand.h"
+#include "removeotulabelscommand.h"
+#include "makecontigscommand.h"
 
 /*******************************************************/
 
@@ -186,8 +195,6 @@ CommandFactory::CommandFactory(){
 	commands["get.label"]           = "get.label";
 	commands["get.sabund"]          = "get.sabund";
 	commands["get.rabund"]          = "get.rabund";
-	commands["bootstrap.shared"]	= "bootstrap.shared";
-	//commands["consensus"]			= "consensus";
 	commands["help"]				= "help";
 	commands["reverse.seqs"]		= "reverse.seqs";
 	commands["trim.seqs"]			= "trim.seqs";
@@ -275,6 +282,17 @@ CommandFactory::CommandFactory(){
 	commands["summary.qual"]		= "summary.qual";
 	commands["shhh.seqs"]			= "shhh.seqs";
 	commands["otu.association"]		= "otu.association";
+    commands["sort.seqs"]           = "sort.seqs";
+    commands["classify.tree"]       = "classify.tree";
+    commands["cooccurrence"]        = "cooccurrence";
+    commands["pcr.seqs"]            = "pcr.seqs";
+    commands["create.database"]     = "create.database";
+    commands["make.biom"]           = "make.biom";
+    commands["get.coremicrobiome"]  = "get.coremicrobiome";
+    commands["list.otulabels"]      = "list.otulabels";
+    commands["get.otulabels"]       = "get.otulabels";
+    commands["remove.otulabels"]    = "remove.otulabels";
+    commands["make.contigs"]        = "make.contigs";
 	commands["quit"]				= "MPIEnabled"; 
 
 }
@@ -298,15 +316,60 @@ CommandFactory::~CommandFactory(){
 	delete shellcommand;
 	delete pipecommand;
 }
+/***********************************************************/
 
+/***********************************************************/
+int CommandFactory::checkForRedirects(string optionString) {
+    try {
+        
+        int pos = optionString.find("outputdir");
+        if (pos != string::npos) { //user has set outputdir in command option string
+            string outputOption = "";
+            bool foundEquals = false;
+            for(int i=pos;i<optionString.length();i++){
+                if(optionString[i] == ',')       { break;               }		
+                else if(optionString[i] == '=')  { foundEquals = true;	}
+                if (foundEquals)       {   outputOption += optionString[i]; }
+            }
+            if(m->dirCheck(outputOption)){ 
+                setOutputDirectory(outputOption); 
+                m->mothurOut("Setting output directory to: " + outputOption); m->mothurOutEndLine();
+            }
+        }
+        
+        pos = optionString.find("inputdir");
+        if (pos != string::npos) { //user has set inputdir in command option string
+            string intputOption = "";
+            bool foundEquals = false;
+            for(int i=pos;i<optionString.length();i++){
+                if(optionString[i] == ',')       { break;               }		
+                else if(optionString[i] == '=')  { foundEquals = true;	}
+                if (foundEquals)       {   intputOption += optionString[i]; }
+            }
+            if(m->dirCheck(intputOption)){ 
+                setInputDirectory(intputOption); 
+                m->mothurOut("Setting input directory to: " + intputOption); m->mothurOutEndLine();
+            }
+        }
+        
+        return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "CommandFactory", "getCommand");
+		exit(1);
+	}
+}
 /***********************************************************/
 
 /***********************************************************/
 //This function calls the appropriate command fucntions based on user input.
 Command* CommandFactory::getCommand(string commandName, string optionString){
 	try {
+        
 		delete command;   //delete the old command
-		
+        
+        checkForRedirects(optionString);
+        		
 		//user has opted to redirect output from dir where input files are located to some other place
 		if (outputDir != "") { 
 			if (optionString != "") { optionString += ", outputdir=" + outputDir; }
@@ -348,8 +411,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "get.oturep")			{   command = new GetOTURepCommand(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 == "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);				}
@@ -436,6 +497,17 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "chimera.perseus")		{	command = new ChimeraPerseusCommand(optionString);			}
 		else if(commandName == "shhh.seqs")				{	command = new ShhhSeqsCommand(optionString);				}
 		else if(commandName == "otu.association")		{	command = new OTUAssociationCommand(optionString);			}
+        else if(commandName == "sort.seqs")             {	command = new SortSeqsCommand(optionString);                }
+        else if(commandName == "classify.tree")         {	command = new ClassifyTreeCommand(optionString);            }
+        else if(commandName == "cooccurrence")          {	command = new CooccurrenceCommand(optionString);            }
+        else if(commandName == "pcr.seqs")              {	command = new PcrSeqsCommand(optionString);                 }
+        else if(commandName == "create.database")       {	command = new CreateDatabaseCommand(optionString);          }
+        else if(commandName == "make.biom")             {	command = new MakeBiomCommand(optionString);                }
+        else if(commandName == "get.coremicrobiome")    {	command = new GetCoreMicroBiomeCommand(optionString);       }
+        else if(commandName == "list.otulabels")        {	command = new ListOtuLabelsCommand(optionString);           }
+        else if(commandName == "get.otulabels")         {	command = new GetOtuLabelsCommand(optionString);            }
+        else if(commandName == "remove.otulabels")      {	command = new RemoveOtuLabelsCommand(optionString);         }
+        else if(commandName == "make.contigs")          {	command = new MakeContigsCommand(optionString);             }
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -453,6 +525,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 	try {
 		delete pipecommand;   //delete the old command
 		
+        checkForRedirects(optionString);
+        
 		//user has opted to redirect output from dir where input files are located to some other place
 		if (outputDir != "") { 
 			if (optionString != "") { optionString += ", outputdir=" + outputDir; }
@@ -494,8 +568,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "get.oturep")			{   pipecommand = new GetOTURepCommand(optionString);				}
 		else if(commandName == "tree.shared")			{   pipecommand = new TreeGroupCommand(optionString);				}
 		else if(commandName == "dist.shared")			{   pipecommand = new MatrixOutputCommand(optionString);			}
-		else if(commandName == "bootstrap.shared")		{   pipecommand = new BootSharedCommand(optionString);				}
-		else if(commandName == "consensus")				{   pipecommand = new ConcensusCommand(optionString);				}
 		else if(commandName == "dist.seqs")				{   pipecommand = new DistanceCommand(optionString);				}
 		else if(commandName == "align.seqs")			{   pipecommand = new AlignCommand(optionString);					}
 		else if(commandName == "summary.seqs")			{	pipecommand = new SeqSummaryCommand(optionString);				}
@@ -581,6 +653,17 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "chimera.perseus")		{	pipecommand = new ChimeraPerseusCommand(optionString);			}
 		else if(commandName == "shhh.seqs")				{	pipecommand = new ShhhSeqsCommand(optionString);				}
 		else if(commandName == "otu.association")		{	pipecommand = new OTUAssociationCommand(optionString);			}
+        else if(commandName == "sort.seqs")             {	pipecommand = new SortSeqsCommand(optionString);                }
+        else if(commandName == "classify.tree")         {	pipecommand = new ClassifyTreeCommand(optionString);            }
+        else if(commandName == "cooccurrence")          {	pipecommand = new CooccurrenceCommand(optionString);            }
+        else if(commandName == "pcr.seqs")              {	pipecommand = new PcrSeqsCommand(optionString);                 }
+        else if(commandName == "create.database")       {	pipecommand = new CreateDatabaseCommand(optionString);          }
+        else if(commandName == "make.biom")             {	pipecommand = new MakeBiomCommand(optionString);                }
+        else if(commandName == "get.coremicrobiome")    {	pipecommand = new GetCoreMicroBiomeCommand(optionString);       }
+        else if(commandName == "list.otulabels")        {	pipecommand = new ListOtuLabelsCommand(optionString);           }
+        else if(commandName == "get.otulabels")         {	pipecommand = new GetOtuLabelsCommand(optionString);            }
+        else if(commandName == "remove.otulabels")      {	pipecommand = new RemoveOtuLabelsCommand(optionString);         }
+        else if(commandName == "make.contigs")          {	pipecommand = new MakeContigsCommand(optionString);             }
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -627,8 +710,6 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "get.oturep")			{   shellcommand = new GetOTURepCommand();				}
 		else if(commandName == "tree.shared")			{   shellcommand = new TreeGroupCommand();				}
 		else if(commandName == "dist.shared")			{   shellcommand = new MatrixOutputCommand();			}
-		else if(commandName == "bootstrap.shared")		{   shellcommand = new BootSharedCommand();				}
-		else if(commandName == "consensus")				{   shellcommand = new ConcensusCommand();				}
 		else if(commandName == "dist.seqs")				{   shellcommand = new DistanceCommand();				}
 		else if(commandName == "align.seqs")			{   shellcommand = new AlignCommand();					}
 		else if(commandName == "summary.seqs")			{	shellcommand = new SeqSummaryCommand();				}
@@ -714,6 +795,17 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "chimera.perseus")		{	shellcommand = new ChimeraPerseusCommand();			}
 		else if(commandName == "shhh.seqs")				{	shellcommand = new ShhhSeqsCommand();				}
 		else if(commandName == "otu.association")		{	shellcommand = new OTUAssociationCommand();			}
+        else if(commandName == "sort.seqs")             {	shellcommand = new SortSeqsCommand();               }
+        else if(commandName == "classify.tree")         {	shellcommand = new ClassifyTreeCommand();           }
+        else if(commandName == "cooccurrence")          {	shellcommand = new CooccurrenceCommand();           }
+        else if(commandName == "pcr.seqs")              {	shellcommand = new PcrSeqsCommand();                }
+        else if(commandName == "create.database")       {	shellcommand = new CreateDatabaseCommand();         }
+        else if(commandName == "make.biom")             {	shellcommand = new MakeBiomCommand();               }
+        else if(commandName == "get.coremicrobiome")    {	shellcommand = new GetCoreMicroBiomeCommand();      }
+        else if(commandName == "list.otulabels")        {	shellcommand = new ListOtuLabelsCommand();          }
+        else if(commandName == "get.otulabels")         {	shellcommand = new GetOtuLabelsCommand();           }
+        else if(commandName == "remove.otulabels")      {	shellcommand = new RemoveOtuLabelsCommand();        }
+        else if(commandName == "make.contigs")          {	shellcommand = new MakeContigsCommand();            }
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;
@@ -739,7 +831,7 @@ Command* CommandFactory::getCommand(){
 		exit(1);
 	}
 }
-/***********************************************************************/
+***********************************************************************/
 bool CommandFactory::isValidCommand(string command) {
 	try {