X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandfactory.cpp;h=e8e9c2754677ee639fce944fbc533d3bd9eb98db;hp=a691509ab0ae00e5f19ae52a8bffe6801fc26a31;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=367747fb506bf228d3b2d645868d275ba0714e90 diff --git a/commandfactory.cpp b/commandfactory.cpp index a691509..e8e9c27 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -135,8 +135,21 @@ #include "makecontigscommand.h" #include "loadlogfilecommand.h" #include "sffmultiplecommand.h" -#include "classifysharedcommand.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" /*******************************************************/ @@ -295,8 +308,21 @@ CommandFactory::CommandFactory(){ commands["make.table"] = "make.table"; commands["sff.multiple"] = "sff.multiple"; commands["quit"] = "MPIEnabled"; - commands["classify.shared"] = "classify.shared"; + 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"; } @@ -386,7 +412,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){ else { optionString += "inputdir=" + inputDir; } } - 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); } @@ -511,8 +537,21 @@ Command* CommandFactory::getCommand(string commandName, string 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.shared") { command = new ClassifySharedCommand(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; @@ -668,8 +707,21 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str 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.shared") { pipecommand = new ClassifySharedCommand(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; @@ -811,8 +863,21 @@ Command* CommandFactory::getCommand(string commandName){ 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.shared") { shellcommand = new ClassifySharedCommand(); } + 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; @@ -892,6 +957,41 @@ void CommandFactory::printCommands(ostream& out) { } } /***********************************************************************/ +void CommandFactory::printCommandsCategories(ostream& out) { + try { + map commands = getListCommands(); + map::iterator it; + + map categories; + map::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); + } +} + +/***********************************************************************/