removing chime source files from mother project.

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index b61c2d2dc820c7cf05b7f82d3983017f2d6d4c55..527f7bfe4fddf6ecf1ddce45ab7c93a161f52ad1 100644 (file)
--- 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"
@@ -132,6 +130,7 @@
 #include "cooccurrencecommand.h"
 #include "pcrseqscommand.h"
 #include "createdatabasecommand.h"
+#include "makebiomcommand.h"
 
 /*******************************************************/
 
@@ -191,8 +190,6 @@ 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";
@@ -285,6 +282,7 @@ CommandFactory::CommandFactory(){
     commands["cooccurrence"]        = "cooccurrence";
     commands["pcr.seqs"]            = "pcr.seqs";
     commands["create.database"]     = "create.database";
+    commands["make.biom"]           = "make.biom";
        commands["quit"]                                = "MPIEnabled"; 
 
 }
@@ -308,7 +306,49 @@ 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);
+       }
+}
 /***********************************************************/
 
 /***********************************************************/
@@ -317,7 +357,9 @@ 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; }
@@ -359,8 +401,6 @@ 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);                          }
@@ -452,6 +492,7 @@ 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                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -469,6 +510,8 @@ 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; }
@@ -510,8 +553,6 @@ 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);                              }
@@ -602,6 +643,7 @@ 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                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -648,8 +690,6 @@ 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();                         }
@@ -740,6 +780,7 @@ 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                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;