added hcluster command and fixed some bugs, namely one with smart distancing.

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 7dd35fd673a7bc62e109a0095efe847d5b097588..5f07abb59e03e161bd46bc60065eb15e37107a06 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -12,7 +12,6 @@
 #include "readtreecommand.h"
 #include "readotucommand.h"
 #include "clustercommand.h"
-#include "parselistcommand.h"
 #include "collectcommand.h"
 #include "collectsharedcommand.h"
 #include "getgroupcommand.h"
@@ -39,7 +38,7 @@
 #include "getoturepcommand.h"
 #include "treegroupscommand.h"
 #include "bootstrapsharedcommand.h"
-#include "concensuscommand.h"
+//#include "consensuscommand.h"
 #include "distancecommand.h"
 #include "aligncommand.h"
 #include "matrixoutputcommand.h"
@@ -50,6 +49,15 @@
 #include "reversecommand.h"
 #include "trimseqscommand.h"
 #include "mergefilecommand.h"
+#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"
 
 /***********************************************************/
 
@@ -89,7 +97,7 @@ CommandFactory::CommandFactory(){
        commands["get.sabund"]          = "get.sabund";
        commands["get.rabund"]          = "get.rabund";
        commands["bootstrap.shared"]    = "bootstrap.shared";
-       commands["concensus"]                   = "concensus";
+       //commands["consensus"]                 = "consensus";
        commands["help"]                                = "help"; 
        commands["filter.seqs"]                 = "filter.seqs";
        commands["align.seqs"]                  = "align.seqs";
@@ -97,7 +105,17 @@ CommandFactory::CommandFactory(){
        commands["screen.seqs"]                 = "screen.seqs";
        commands["reverse.seqs"]                = "reverse.seqs";
        commands["trim.seqs"]                   = "trim.seqs";
+       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.sharedotu"]               = "get.sharedotu";
+       commands["get.listcount"]               = "get.listcount";
        commands["quit"]                                = "quit"; 
+       
+       commands["hcluster"]                    = "hcluster"; 
 
 }
 /***********************************************************/
@@ -146,27 +164,32 @@ Command* CommandFactory::getCommand(string commandName, string 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 == "concensus")                             {   command = new ConcensusCommand(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);                  }
                else if(commandName == "screen.seqs")                   {       command = new ScreenSeqsCommand(optionString);                  }
                else if(commandName == "reverse.seqs")                  {       command = new ReverseSeqsCommand(optionString);                 }
                else if(commandName == "trim.seqs")                             {       command = new TrimSeqsCommand(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.sharedotu")                 {       command = new GetSharedOTUCommand(optionString);                }
+               else if(commandName == "get.listcount")                 {       command = new GetListCountCommand(optionString);                }
+               
+               else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                    }
                else                                                                                    {       command = new NoCommand(optionString);                                  }
 
                return command;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "CommandFactory", "getCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the CommandFactory class function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-
 }
 
 /***********************************************************************/
@@ -177,21 +200,17 @@ bool CommandFactory::isValidCommand(string command) {
                if ((commands.find(command)) != (commands.end())) {
                        return true;
                }else{
-                       cout << command << " is not a valid command in Mothur.  Valid commands are ";
+                       mothurOut(command + " is not a valid command in Mothur.  Valid commands are ");
                        for (it = commands.begin(); it != commands.end(); it++) {
-                               cout << it->first << ", ";
+                               mothurOut(it->first + ", ");
                        }
-                       cout << endl;
+                       mothurOutEndLine();
                        return false;
                }
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the CommandFactory class function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "CommandFactory", "isValidCommand");
                exit(1);
        }
 }
@@ -206,11 +225,7 @@ void CommandFactory::printCommands(ostream& out) {
                out << endl;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the CommandFactory class function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "CommandFactory", "printCommands");
                exit(1);
        }
 }