X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandfactory.cpp;h=387ee10833323300a66a0e6d1161a64bff6fb9ee;hp=1241a04e998537fe33446a1c9ba3d933e690e557;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=ccf2fedbb600a362777a11501bb56c9c7746068e diff --git a/commandfactory.cpp b/commandfactory.cpp index 1241a04..387ee10 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" @@ -133,7 +130,20 @@ #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 "classifysharedcommand.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" /*******************************************************/ @@ -166,9 +176,6 @@ 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"; @@ -288,8 +295,23 @@ CommandFactory::CommandFactory(){ 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.shared"] = "classify.shared"; + 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.metacommunity"] = "get.metacommunity"; + commands["sparcc"] = "sparcc"; + commands["make.lookup"] = "make.lookup"; + } /***********************************************************/ @@ -378,10 +400,7 @@ 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); } @@ -485,7 +504,7 @@ 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); } @@ -501,7 +520,20 @@ Command* CommandFactory::getCommand(string commandName, string 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.shared") { command = new ClassifySharedCommand(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.metacommunity") { command = new GetMetaCommunityCommand(optionString); } + else if(commandName == "sparcc") { command = new SparccCommand(optionString); } + else if(commandName == "make.lookup") { command = new MakeLookupCommand(optionString); } else { command = new NoCommand(optionString); } return command; @@ -533,10 +565,7 @@ 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); } @@ -639,7 +668,7 @@ 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); } @@ -655,7 +684,20 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str 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.shared") { pipecommand = new ClassifySharedCommand(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.metacommunity") { pipecommand = new GetMetaCommunityCommand(optionString); } + else if(commandName == "sparcc") { pipecommand = new SparccCommand(optionString); } + else if(commandName == "make.lookup") { pipecommand = new MakeLookupCommand(optionString); } else { pipecommand = new NoCommand(optionString); } return pipecommand; @@ -673,10 +715,7 @@ 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(); } @@ -779,7 +818,7 @@ 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(); } @@ -795,7 +834,20 @@ Command* CommandFactory::getCommand(string commandName){ 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.shared") { shellcommand = new ClassifySharedCommand(); } + 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.metacommunity") { shellcommand = new GetMetaCommunityCommand(); } + else if(commandName == "sparcc") { shellcommand = new SparccCommand(); } + else if(commandName == "make.lookup") { shellcommand = new MakeLookupCommand(); } else { shellcommand = new NoCommand(); } return shellcommand; @@ -875,6 +927,41 @@ 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); + } +} + +/***********************************************************************/