modified sequence class to read fasta files with comments. this required modification...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 635cff032a645b7e69c168c7b461eaca71bb364d..a3858639a1f78d633e9c1537054978bac4e4d499 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -181,7 +181,7 @@ Command* CommandFactory::getCommand(string commandName, string 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.sharedseqs")                        {       command = new GetSharedOTUCommand(optionString);                }
+               else if(commandName == "get.sharedseqs")                {       command = new GetSharedOTUCommand(optionString);                }
                else if(commandName == "get.otulist")                   {       command = new GetListCountCommand(optionString);                }
                else if(commandName == "hcluster")                              {       command = new HClusterCommand(optionString);                    }
                else if(commandName == "classify.seqs")                 {       command = new ClassifySeqsCommand(optionString);                }
@@ -195,7 +195,22 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                exit(1);
        }
 }
+/***********************************************************/
+//This function is used to interrupt a command
+Command* CommandFactory::getCommand(){
+       try {
+               delete command;   //delete the old command
 
+               string s = "";
+           command = new NoCommand(s);
+       
+               return command;
+       }
+       catch(exception& e) {
+               errorOut(e, "CommandFactory", "getCommand");
+               exit(1);
+       }
+}
 /***********************************************************************/
 bool CommandFactory::isValidCommand(string command) {
        try {