X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandfactory.cpp;h=e8e9c2754677ee639fce944fbc533d3bd9eb98db;hp=0c9504d09a109a39168af9b9d582ef20732e6647;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=bb8d942036365d2a66330944269f17841ed2388a

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 0c9504d..e8e9c27 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -8,9 +8,6 @@
  */
 
 #include "command.hpp"
-#include "readdistcommand.h"
-#include "readtreecommand.h"
-#include "readotucommand.h"
 #include "clustercommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
@@ -130,6 +127,29 @@
 #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"
+#include "loadlogfilecommand.h"
+#include "sffmultiplecommand.h"
+#include "classifyrfsharedcommand.h"
+#include "filtersharedcommand.h"
+#include "primerdesigncommand.h"
+#include "getdistscommand.h"
+#include "removedistscommand.h"
+#include "mergetaxsummarycommand.h"
+#include "getmetacommunitycommand.h"
+#include "sparcccommand.h"
+#include "makelookupcommand.h"
+#include "renameseqscommand.h"
+#include "makelefsecommand.h"
+#include "lefsecommand.h"
+#include "kruskalwalliscommand.h"
+#include "sracommand.h"
+#include "mergesfffilecommand.h"
 
 /*******************************************************/
 
@@ -162,9 +182,6 @@ CommandFactory::CommandFactory(){
 	append = false;
 	
 	//initialize list of valid commands
-	commands["read.dist"]			= "read.dist"; 
-	commands["read.otu"]			= "read.otu";
-	commands["read.tree"]			= "read.tree"; 
 	commands["make.shared"]			= "make.shared"; 
 	commands["bin.seqs"]			= "bin.seqs"; 
 	commands["get.oturep"]			= "get.oturep";
@@ -281,7 +298,32 @@ CommandFactory::CommandFactory(){
     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["load.logfile"]        = "load.logfile";
+    commands["make.table"]          = "make.table";
+    commands["sff.multiple"]        = "sff.multiple";
 	commands["quit"]				= "MPIEnabled"; 
+    commands["classify.rf"]         = "classify.rf"; 
+    commands["filter.shared"]		= "filter.shared"; 
+    commands["primer.design"]		= "primer.design";
+    commands["get.dists"]           = "get.dists";
+    commands["remove.dists"]        = "remove.dists";
+    commands["merge.taxsummary"]    = "merge.taxsummary";
+    commands["get.communitytype"]   = "get.communitytype";
+    commands["sparcc"]              = "sparcc";
+    commands["make.lookup"]         = "make.lookup";
+    commands["rename.seqs"]         = "rename.seqs";
+    commands["make.lefse"]          = "make.lefse";
+    commands["lefse"]               = "lefse";
+    commands["kruskal.wallis"]      = "kruskal.wallis";
+    commands["sra"]                 = "sra";
+    commands["merge.sfffiles"]      = "merge.sfffiles";
+    
 
 }
 /***********************************************************/
@@ -304,7 +346,49 @@ 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);
+	}
+}
 /***********************************************************/
 
 /***********************************************************/
@@ -313,7 +397,9 @@ 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; }
@@ -326,10 +412,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 			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 == "cluster")				{	command = new ClusterCommand(optionString);					}
+		if(commandName == "cluster")                    {	command = new ClusterCommand(optionString);					}
 		else if(commandName == "unique.seqs")			{	command = new DeconvoluteCommand(optionString);				}
 		else if(commandName == "parsimony")				{	command = new ParsimonyCommand(optionString);				}
 		else if(commandName == "help")					{	command = new HelpCommand(optionString);					}
@@ -433,7 +516,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "make.shared")			{	command = new SharedCommand(optionString);					}
 		else if(commandName == "get.commandinfo")		{	command = new GetCommandInfoCommand(optionString);			}
 		else if(commandName == "deunique.tree")			{	command = new DeuniqueTreeCommand(optionString);			}
-		else if(commandName == "count.seqs")			{	command = new CountSeqsCommand(optionString);				}
+		else if((commandName == "count.seqs") || (commandName == "make.table"))			{	command = new CountSeqsCommand(optionString);				}
 		else if(commandName == "count.groups")			{	command = new CountGroupsCommand(optionString);				}
 		else if(commandName == "clear.memory")			{	command = new ClearMemoryCommand(optionString);				}
 		else if(commandName == "summary.tax")			{	command = new SummaryTaxCommand(optionString);				}
@@ -446,6 +529,29 @@ Command* CommandFactory::getCommand(string commandName, string 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 if(commandName == "load.logfile")          {	command = new LoadLogfileCommand(optionString);             }
+        else if(commandName == "sff.multiple")          {	command = new SffMultipleCommand(optionString);             }
+        else if(commandName == "classify.rf")           {	command = new ClassifyRFSharedCommand(optionString);        }
+        else if(commandName == "filter.shared")         {	command = new FilterSharedCommand(optionString);            }
+        else if(commandName == "primer.design")         {	command = new PrimerDesignCommand(optionString);            }
+        else if(commandName == "get.dists")             {	command = new GetDistsCommand(optionString);                }
+        else if(commandName == "remove.dists")          {	command = new RemoveDistsCommand(optionString);             }
+        else if(commandName == "merge.taxsummary")      {	command = new MergeTaxSummaryCommand(optionString);         }
+        else if(commandName == "get.communitytype")     {	command = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "sparcc")                {	command = new SparccCommand(optionString);                  }
+        else if(commandName == "make.lookup")			{	command = new MakeLookupCommand(optionString);				}
+        else if(commandName == "rename.seqs")			{	command = new RenameSeqsCommand(optionString);				}
+        else if(commandName == "make.lefse")			{	command = new MakeLefseCommand(optionString);				}
+        else if(commandName == "lefse")                 {	command = new LefseCommand(optionString);                   }
+        else if(commandName == "kruskal.wallis")        {	command = new KruskalWallisCommand(optionString);           }
+        else if(commandName == "sra")                   {	command = new SRACommand(optionString);                     }
+        else if(commandName == "merge.sfffiles")        {	command = new MergeSfffilesCommand(optionString);           }
 		else											{	command = new NoCommand(optionString);						}
 
 		return command;
@@ -463,6 +569,8 @@ 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; }
@@ -475,10 +583,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 			else { optionString += "inputdir=" + inputDir; }
 		}
 		
-		if(commandName == "read.dist")					{	pipecommand = new ReadDistCommand(optionString);				}
-		else if(commandName == "read.otu")				{	pipecommand = new ReadOtuCommand(optionString);					}
-		else if(commandName == "read.tree")				{	pipecommand = new ReadTreeCommand(optionString);				}
-		else if(commandName == "cluster")				{	pipecommand = new ClusterCommand(optionString);					}
+		if(commandName == "cluster")				{	pipecommand = new ClusterCommand(optionString);					}
 		else if(commandName == "unique.seqs")			{	pipecommand = new DeconvoluteCommand(optionString);				}
 		else if(commandName == "parsimony")				{	pipecommand = new ParsimonyCommand(optionString);				}
 		else if(commandName == "help")					{	pipecommand = new HelpCommand(optionString);					}
@@ -581,7 +686,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "make.shared")			{	pipecommand = new SharedCommand(optionString);					}
 		else if(commandName == "get.commandinfo")		{	pipecommand = new GetCommandInfoCommand(optionString);			}
 		else if(commandName == "deunique.tree")			{	pipecommand = new DeuniqueTreeCommand(optionString);			}
-		else if(commandName == "count.seqs")			{	pipecommand = new CountSeqsCommand(optionString);				}
+		else if((commandName == "count.seqs") || (commandName == "make.table"))			{	pipecommand = new CountSeqsCommand(optionString);				}
 		else if(commandName == "count.groups")			{	pipecommand = new CountGroupsCommand(optionString);				}
 		else if(commandName == "clear.memory")			{	pipecommand = new ClearMemoryCommand(optionString);				}
 		else if(commandName == "summary.tax")			{	pipecommand = new SummaryTaxCommand(optionString);				}
@@ -594,6 +699,29 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         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 if(commandName == "load.logfile")          {	pipecommand = new LoadLogfileCommand(optionString);             }
+        else if(commandName == "sff.multiple")          {	pipecommand = new SffMultipleCommand(optionString);             }
+        else if(commandName == "classify.rf")           {	pipecommand = new ClassifyRFSharedCommand(optionString);        }
+        else if(commandName == "filter.shared")         {	pipecommand = new FilterSharedCommand(optionString);            }
+        else if(commandName == "primer.design")         {	pipecommand = new PrimerDesignCommand(optionString);            }
+        else if(commandName == "get.dists")             {	pipecommand = new GetDistsCommand(optionString);                }
+        else if(commandName == "remove.dists")          {	pipecommand = new RemoveDistsCommand(optionString);             }
+        else if(commandName == "merge.taxsummary")      {	pipecommand = new MergeTaxSummaryCommand(optionString);         }
+        else if(commandName == "get.communitytype")     {	pipecommand = new GetMetaCommunityCommand(optionString);        }
+        else if(commandName == "sparcc")                {	pipecommand = new SparccCommand(optionString);                  }
+        else if(commandName == "make.lookup")			{	pipecommand = new MakeLookupCommand(optionString);				}
+        else if(commandName == "rename.seqs")			{	pipecommand = new RenameSeqsCommand(optionString);				}
+        else if(commandName == "make.lefse")			{	pipecommand = new MakeLefseCommand(optionString);				}
+        else if(commandName == "lefse")                 {	pipecommand = new LefseCommand(optionString);                   }
+        else if(commandName == "kruskal.wallis")        {	pipecommand = new KruskalWallisCommand(optionString);           }
+        else if(commandName == "sra")                   {	pipecommand = new SRACommand(optionString);                     }
+        else if(commandName == "merge.sfffiles")        {	pipecommand = new MergeSfffilesCommand(optionString);           }
 		else											{	pipecommand = new NoCommand(optionString);						}
 
 		return pipecommand;
@@ -611,10 +739,7 @@ Command* CommandFactory::getCommand(string commandName){
 	try {
 		delete shellcommand;   //delete the old command
 		
-		if(commandName == "read.dist")					{	shellcommand = new ReadDistCommand();				}
-		else if(commandName == "read.otu")				{	shellcommand = new ReadOtuCommand();				}
-		else if(commandName == "read.tree")				{	shellcommand = new ReadTreeCommand();				}
-		else if(commandName == "cluster")				{	shellcommand = new ClusterCommand();				}
+		if(commandName == "cluster")				{	shellcommand = new ClusterCommand();				}
 		else if(commandName == "unique.seqs")			{	shellcommand = new DeconvoluteCommand();			}
 		else if(commandName == "parsimony")				{	shellcommand = new ParsimonyCommand();				}
 		else if(commandName == "help")					{	shellcommand = new HelpCommand();					}
@@ -717,7 +842,7 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "make.shared")			{	shellcommand = new SharedCommand();					}
 		else if(commandName == "get.commandinfo")		{	shellcommand = new GetCommandInfoCommand();			}
 		else if(commandName == "deunique.tree")			{	shellcommand = new DeuniqueTreeCommand();			}
-		else if(commandName == "count.seqs")			{	shellcommand = new CountSeqsCommand();				}
+		else if((commandName == "count.seqs") || (commandName == "make.table"))			{	shellcommand = new CountSeqsCommand();				}
 		else if(commandName == "count.groups")			{	shellcommand = new CountGroupsCommand();			}
 		else if(commandName == "clear.memory")			{	shellcommand = new ClearMemoryCommand();			}
 		else if(commandName == "summary.tax")			{	shellcommand = new SummaryTaxCommand();				}
@@ -730,6 +855,29 @@ Command* CommandFactory::getCommand(string commandName){
         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 if(commandName == "load.logfile")          {	shellcommand = new LoadLogfileCommand();            }
+        else if(commandName == "sff.multiple")          {	shellcommand = new SffMultipleCommand();            }
+        else if(commandName == "classify.rf")           {	shellcommand = new ClassifyRFSharedCommand();       }
+        else if(commandName == "filter.shared")         {	shellcommand = new FilterSharedCommand();           }
+        else if(commandName == "primer.design")         {	shellcommand = new PrimerDesignCommand();           }
+        else if(commandName == "get.dists")             {	shellcommand = new GetDistsCommand();               }
+        else if(commandName == "remove.dists")          {	shellcommand = new RemoveDistsCommand();            }
+        else if(commandName == "merge.taxsummary")      {	shellcommand = new MergeTaxSummaryCommand();        }
+        else if(commandName == "get.communitytype")     {	shellcommand = new GetMetaCommunityCommand();       }
+        else if(commandName == "sparcc")                {	shellcommand = new SparccCommand();                 }
+        else if(commandName == "make.lookup")			{	shellcommand = new MakeLookupCommand();				}
+        else if(commandName == "rename.seqs")			{	shellcommand = new RenameSeqsCommand();				}
+        else if(commandName == "make.lefse")			{	shellcommand = new MakeLefseCommand();				}
+        else if(commandName == "lefse")                 {	shellcommand = new LefseCommand();                  }
+        else if(commandName == "kruskal.wallis")        {	shellcommand = new KruskalWallisCommand();          }
+        else if(commandName == "sra")                   {	shellcommand = new SRACommand();                    }
+        else if(commandName == "merge.sfffiles")        {	shellcommand = new MergeSfffilesCommand();          }
 		else											{	shellcommand = new NoCommand();						}
 
 		return shellcommand;
@@ -809,6 +957,41 @@ void CommandFactory::printCommands(ostream& out) {
 	}
 }
 /***********************************************************************/
+void CommandFactory::printCommandsCategories(ostream& out) {
+    try {
+        map<string, string> commands = getListCommands();
+        map<string, string>::iterator it;
+
+        map<string, string> categories;
+        map<string, string>::iterator itCat;
+        //loop through each command outputting info
+        for (it = commands.begin(); it != commands.end(); it++) {
+    
+            Command* thisCommand = getCommand(it->first);
+    
+            //don't add hidden commands
+            if (thisCommand->getCommandCategory() != "Hidden") {
+                itCat = categories.find(thisCommand->getCommandCategory());
+                if (itCat == categories.end()) {
+                    categories[thisCommand->getCommandCategory()] = thisCommand->getCommandName();
+                }else {
+                    categories[thisCommand->getCommandCategory()] += ", " + thisCommand->getCommandName();
+                }
+            }
+        }
+        
+        for (itCat = categories.begin(); itCat != categories.end(); itCat++) {
+            out << itCat->first << " commmands include: " << itCat->second << endl;
+        }
+
+    }
+	catch(exception& e) {
+		m->errorOut(e, "CommandFactory", "printCommandsCategories");
+		exit(1);
+	}
+}      
+
+/***********************************************************************/