X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=6d87a68c49c6d9154572adcbc51ebc3b4555a35f;hb=16f9c4ab6f39769856b13e048eae2c8eaa413c02;hp=c334b095abbc65a5bd9e40cc6f2160f6c37d3e2e;hpb=42d411d3362186465347aeabdd3155bd3259671e;p=mothur.git diff --git a/commandfactory.cpp b/commandfactory.cpp index c334b09..6d87a68 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" @@ -131,7 +128,14 @@ #include "pcrseqscommand.h" #include "createdatabasecommand.h" #include "makebiomcommand.h" -#include "getcoremicrobiomcommand.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" /*******************************************************/ @@ -164,9 +168,6 @@ 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"; @@ -284,8 +285,17 @@ CommandFactory::CommandFactory(){ commands["pcr.seqs"] = "pcr.seqs"; commands["create.database"] = "create.database"; commands["make.biom"] = "make.biom"; - commands["get.coremicrobiom"] = "get.coremircrobiom"; + 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"; + } /***********************************************************/ @@ -374,10 +384,7 @@ 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); } @@ -481,7 +488,7 @@ 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); } @@ -495,7 +502,14 @@ Command* CommandFactory::getCommand(string commandName, string 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 if(commandName == "get.coremicrobiom") { command = new GetCoreMicroBiomCommand(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 { command = new NoCommand(optionString); } return command; @@ -527,10 +541,7 @@ 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); } @@ -633,7 +644,7 @@ 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); } @@ -647,7 +658,14 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str 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 if(commandName == "get.coremicrobiom") { pipecommand = new GetCoreMicroBiomCommand(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 { pipecommand = new NoCommand(optionString); } return pipecommand; @@ -665,10 +683,7 @@ 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(); } @@ -771,7 +786,7 @@ 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(); } @@ -785,7 +800,14 @@ Command* CommandFactory::getCommand(string commandName){ 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 if(commandName == "get.coremicrobiom") { shellcommand = new GetCoreMicroBiomCommand(); } + 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 { shellcommand = new NoCommand(); } return shellcommand;