X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=71558a9292280dcc9f28acb29b2944fb62a05eb6;hb=0cc0c01eb5127ef2b09b894e1f224ccc1d70bef0;hp=924e3f78479f449d09a6ce6d9bd3985aa846409c;hpb=17d3033f832c6b8fff5875eb4de29f44a926d4dd;p=mothur.git diff --git a/commandfactory.cpp b/commandfactory.cpp index 924e3f7..71558a9 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -48,7 +48,6 @@ #include "reversecommand.h" #include "trimseqscommand.h" #include "mergefilecommand.h" -#include "chimeraseqscommand.h" #include "listseqscommand.h" #include "getseqscommand.h" #include "removeseqscommand.h" @@ -70,6 +69,7 @@ #include "chimeraslayercommand.h" #include "chimerapintailcommand.h" #include "chimerabellerophoncommand.h" +#include "chimerauchimecommand.h" #include "setlogfilecommand.h" #include "phylodiversitycommand.h" #include "makegroupcommand.h" @@ -111,6 +111,14 @@ #include "mergegroupscommand.h" #include "amovacommand.h" #include "homovacommand.h" +#include "mantelcommand.h" +#include "makefastqcommand.h" +#include "anosimcommand.h" +#include "getcurrentcommand.h" +#include "setcurrentcommand.h" +#include "sharedcommand.h" +#include "getcommandinfocommand.h" +#include "deuniquetreecommand.h" /*******************************************************/ @@ -146,6 +154,7 @@ CommandFactory::CommandFactory(){ 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"; commands["cluster"] = "cluster"; @@ -177,7 +186,7 @@ CommandFactory::CommandFactory(){ commands["trim.flows"] = "trim.flows"; commands["list.seqs"] = "list.seqs"; commands["get.seqs"] = "get.seqs"; - commands["remove.seqs"] = "get.seqs"; + commands["remove.seqs"] = "remove.seqs"; commands["system"] = "system"; commands["align.check"] = "align.check"; commands["get.sharedseqs"] = "get.sharedseqs"; @@ -224,17 +233,24 @@ CommandFactory::CommandFactory(){ commands["remove.rare"] = "remove.rare"; commands["amova"] = "amova"; commands["homova"] = "homova"; + commands["mantel"] = "mantel"; + commands["anosim"] = "anosim"; + commands["make.fastq"] = "make.fastq"; commands["merge.groups"] = "merge.groups"; + commands["get.current"] = "get.current"; + commands["set.current"] = "set.current"; + commands["get.commandinfo"] = "get.commandinfo"; + commands["deunique.tree"] = "deunique.tree"; commands["pairwise.seqs"] = "MPIEnabled"; commands["pipeline.pds"] = "MPIEnabled"; commands["classify.seqs"] = "MPIEnabled"; commands["dist.seqs"] = "MPIEnabled"; commands["filter.seqs"] = "MPIEnabled"; commands["align.seqs"] = "MPIEnabled"; - commands["chimera.seqs"] = "chimera.seqs"; commands["chimera.ccode"] = "MPIEnabled"; commands["chimera.check"] = "MPIEnabled"; commands["chimera.slayer"] = "MPIEnabled"; + commands["chimera.uchime"] = "MPIEnabled"; commands["chimera.pintail"] = "MPIEnabled"; commands["chimera.bellerophon"] = "MPIEnabled"; commands["screen.seqs"] = "MPIEnabled"; @@ -326,7 +342,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString){ else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(optionString); } else if(commandName == "trim.flows") { command = new TrimFlowsCommand(optionString); } else if(commandName == "shhh.seqs") { command = new ShhherCommand(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); } @@ -340,6 +355,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){ else if(commandName == "chimera.ccode") { command = new ChimeraCcodeCommand(optionString); } else if(commandName == "chimera.check") { command = new ChimeraCheckCommand(optionString); } else if(commandName == "chimera.slayer") { command = new ChimeraSlayerCommand(optionString); } + else if(commandName == "chimera.uchime") { command = new ChimeraUchimeCommand(optionString); } else if(commandName == "chimera.pintail") { command = new ChimeraPintailCommand(optionString); } else if(commandName == "chimera.bellerophon") { command = new ChimeraBellerophonCommand(optionString); } else if(commandName == "phylotype") { command = new PhylotypeCommand(optionString); } @@ -388,6 +404,14 @@ Command* CommandFactory::getCommand(string commandName, string optionString){ else if(commandName == "merge.groups") { command = new MergeGroupsCommand(optionString); } else if(commandName == "amova") { command = new AmovaCommand(optionString); } else if(commandName == "homova") { command = new HomovaCommand(optionString); } + else if(commandName == "mantel") { command = new MantelCommand(optionString); } + else if(commandName == "make.fastq") { command = new MakeFastQCommand(optionString); } + else if(commandName == "get.current") { command = new GetCurrentCommand(optionString); } + else if(commandName == "set.current") { command = new SetCurrentCommand(optionString); } + else if(commandName == "anosim") { command = new AnosimCommand(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 { command = new NoCommand(optionString); } return command; @@ -456,7 +480,6 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str else if(commandName == "trim.seqs") { pipecommand = new TrimSeqsCommand(optionString); } else if(commandName == "trim.flows") { pipecommand = new TrimFlowsCommand(optionString); } else if(commandName == "shhh.seqs") { pipecommand = new ShhherCommand(optionString); } - else if(commandName == "chimera.seqs") { pipecommand = new ChimeraSeqsCommand(optionString); } else if(commandName == "list.seqs") { pipecommand = new ListSeqsCommand(optionString); } else if(commandName == "get.seqs") { pipecommand = new GetSeqsCommand(optionString); } else if(commandName == "remove.seqs") { pipecommand = new RemoveSeqsCommand(optionString); } @@ -469,6 +492,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str else if(commandName == "classify.seqs") { pipecommand = new ClassifySeqsCommand(optionString); } else if(commandName == "chimera.ccode") { pipecommand = new ChimeraCcodeCommand(optionString); } else if(commandName == "chimera.check") { pipecommand = new ChimeraCheckCommand(optionString); } + else if(commandName == "chimera.uchime") { pipecommand = new ChimeraUchimeCommand(optionString); } else if(commandName == "chimera.slayer") { pipecommand = new ChimeraSlayerCommand(optionString); } else if(commandName == "chimera.pintail") { pipecommand = new ChimeraPintailCommand(optionString); } else if(commandName == "chimera.bellerophon") { pipecommand = new ChimeraBellerophonCommand(optionString); } @@ -517,6 +541,14 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str else if(commandName == "merge.groups") { pipecommand = new MergeGroupsCommand(optionString); } else if(commandName == "amova") { pipecommand = new AmovaCommand(optionString); } else if(commandName == "homova") { pipecommand = new HomovaCommand(optionString); } + else if(commandName == "mantel") { pipecommand = new MantelCommand(optionString); } + else if(commandName == "anosim") { pipecommand = new AnosimCommand(optionString); } + else if(commandName == "make.fastq") { pipecommand = new MakeFastQCommand(optionString); } + else if(commandName == "get.current") { pipecommand = new GetCurrentCommand(optionString); } + else if(commandName == "set.current") { pipecommand = new SetCurrentCommand(optionString); } + 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 { pipecommand = new NoCommand(optionString); } return pipecommand; @@ -573,7 +605,6 @@ Command* CommandFactory::getCommand(string commandName){ else if(commandName == "trim.seqs") { shellcommand = new TrimSeqsCommand(); } else if(commandName == "trim.flows") { shellcommand = new TrimFlowsCommand(); } else if(commandName == "shhh.seqs") { shellcommand = new ShhherCommand(); } - else if(commandName == "chimera.seqs") { shellcommand = new ChimeraSeqsCommand(); } else if(commandName == "list.seqs") { shellcommand = new ListSeqsCommand(); } else if(commandName == "get.seqs") { shellcommand = new GetSeqsCommand(); } else if(commandName == "remove.seqs") { shellcommand = new RemoveSeqsCommand(); } @@ -587,6 +618,7 @@ Command* CommandFactory::getCommand(string commandName){ else if(commandName == "chimera.ccode") { shellcommand = new ChimeraCcodeCommand(); } else if(commandName == "chimera.check") { shellcommand = new ChimeraCheckCommand(); } else if(commandName == "chimera.slayer") { shellcommand = new ChimeraSlayerCommand(); } + else if(commandName == "chimera.uchime") { shellcommand = new ChimeraUchimeCommand(); } else if(commandName == "chimera.pintail") { shellcommand = new ChimeraPintailCommand(); } else if(commandName == "chimera.bellerophon") { shellcommand = new ChimeraBellerophonCommand(); } else if(commandName == "phylotype") { shellcommand = new PhylotypeCommand(); } @@ -634,6 +666,14 @@ Command* CommandFactory::getCommand(string commandName){ else if(commandName == "merge.groups") { shellcommand = new MergeGroupsCommand(); } else if(commandName == "amova") { shellcommand = new AmovaCommand(); } else if(commandName == "homova") { shellcommand = new HomovaCommand(); } + else if(commandName == "mantel") { shellcommand = new MantelCommand(); } + else if(commandName == "anosim") { shellcommand = new AnosimCommand(); } + else if(commandName == "make.fastq") { shellcommand = new MakeFastQCommand(); } + else if(commandName == "get.current") { shellcommand = new GetCurrentCommand(); } + else if(commandName == "set.current") { shellcommand = new SetCurrentCommand(); } + 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 { shellcommand = new NoCommand(); } return shellcommand;