X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=commandfactory.cpp;h=303bf084c15b6d2f525ed70152348374b00f03b0;hb=d9c3ceb4147b827719046c7d742df14288a07722;hp=a04ee160bb92870aa05865fc25e7504f8a689596;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git diff --git a/commandfactory.cpp b/commandfactory.cpp index a04ee16..303bf08 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -8,9 +8,9 @@ */ #include "command.hpp" -//#include "readdistcommand.h" -//#include "readtreecommand.h" -//#include "readotucommand.h" +#include "readdistcommand.h" +#include "readtreecommand.h" +#include "readotucommand.h" #include "clustercommand.h" #include "collectcommand.h" #include "collectsharedcommand.h" @@ -69,6 +69,7 @@ #include "chimeraslayercommand.h" #include "chimerapintailcommand.h" #include "chimerabellerophoncommand.h" +#include "chimerauchimecommand.h" #include "setlogfilecommand.h" #include "phylodiversitycommand.h" #include "makegroupcommand.h" @@ -116,6 +117,18 @@ #include "getcurrentcommand.h" #include "setcurrentcommand.h" #include "sharedcommand.h" +#include "getcommandinfocommand.h" +#include "deuniquetreecommand.h" +#include "countseqscommand.h" +#include "countgroupscommand.h" +#include "clearmemorycommand.h" +#include "summarytaxcommand.h" +#include "chimeraperseuscommand.h" +#include "shhhseqscommand.h" +#include "summaryqualcommand.h" +#include "otuassociationcommand.h" +#include "sortseqscommand.h" +#include "classifytreecommand.h" /*******************************************************/ @@ -148,9 +161,9 @@ 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["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"; @@ -183,7 +196,7 @@ 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"; @@ -194,7 +207,7 @@ CommandFactory::CommandFactory(){ commands["pre.cluster"] = "pre.cluster"; commands["pcoa"] = "pcoa"; commands["otu.hierarchy"] = "otu.hierarchy"; - commands["set.dir"] = "set.dir"; + commands["set.dir"] = "MPIEnabled"; commands["merge.files"] = "merge.files"; commands["parse.list"] = "parse.list"; commands["set.logfile"] = "set.logfile"; @@ -234,8 +247,13 @@ CommandFactory::CommandFactory(){ 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.current"] = "MPIEnabled"; + commands["set.current"] = "MPIEnabled"; + commands["get.commandinfo"] = "get.commandinfo"; + commands["deunique.tree"] = "deunique.tree"; + commands["count.seqs"] = "count.seqs"; + commands["count.groups"] = "count.groups"; + commands["clear.memory"] = "clear.memory"; commands["pairwise.seqs"] = "MPIEnabled"; commands["pipeline.pds"] = "MPIEnabled"; commands["classify.seqs"] = "MPIEnabled"; @@ -245,14 +263,22 @@ CommandFactory::CommandFactory(){ commands["chimera.ccode"] = "MPIEnabled"; commands["chimera.check"] = "MPIEnabled"; commands["chimera.slayer"] = "MPIEnabled"; + commands["chimera.uchime"] = "chimera.uchime"; + commands["chimera.perseus"] = "chimera.perseus"; commands["chimera.pintail"] = "MPIEnabled"; commands["chimera.bellerophon"] = "MPIEnabled"; commands["screen.seqs"] = "MPIEnabled"; commands["summary.seqs"] = "MPIEnabled"; commands["cluster.split"] = "MPIEnabled"; - commands["shhh.seqs"] = "MPIEnabled"; + commands["shhh.flows"] = "MPIEnabled"; commands["sens.spec"] = "sens.spec"; commands["seq.error"] = "seq.error"; + commands["summary.tax"] = "summary.tax"; + commands["summary.qual"] = "summary.qual"; + commands["shhh.seqs"] = "shhh.seqs"; + commands["otu.association"] = "otu.association"; + commands["sort.seqs"] = "sort.seqs"; + commands["classify.tree"] = "classify.tree"; commands["quit"] = "MPIEnabled"; } @@ -297,10 +323,10 @@ 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); } - if(commandName == "cluster") { command = new ClusterCommand(optionString); } + 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); } 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); } @@ -335,7 +361,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){ else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(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 == "shhh.flows") { command = new ShhherCommand(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); } @@ -349,6 +375,7 @@ 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); } @@ -403,6 +430,18 @@ Command* CommandFactory::getCommand(string commandName, string 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 if(commandName == "count.seqs") { 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); } + else if(commandName == "summary.qual") { command = new SummaryQualCommand(optionString); } + else if(commandName == "chimera.perseus") { command = new ChimeraPerseusCommand(optionString); } + else if(commandName == "shhh.seqs") { command = new ShhhSeqsCommand(optionString); } + else if(commandName == "otu.association") { command = new OTUAssociationCommand(optionString); } + else if(commandName == "sort.seqs") { command = new SortSeqsCommand(optionString); } + else if(commandName == "classify.tree") { command = new ClassifyTreeCommand(optionString); } else { command = new NoCommand(optionString); } return command; @@ -432,10 +471,10 @@ 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); } - if(commandName == "cluster") { pipecommand = new ClusterCommand(optionString); } + 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); } 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); } @@ -470,7 +509,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str else if(commandName == "reverse.seqs") { pipecommand = new ReverseSeqsCommand(optionString); } 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 == "shhh.flows") { pipecommand = new ShhherCommand(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); } @@ -483,6 +522,7 @@ 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); } @@ -537,6 +577,18 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str 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 if(commandName == "count.seqs") { 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); } + else if(commandName == "summary.qual") { pipecommand = new SummaryQualCommand(optionString); } + else if(commandName == "chimera.perseus") { pipecommand = new ChimeraPerseusCommand(optionString); } + else if(commandName == "shhh.seqs") { pipecommand = new ShhhSeqsCommand(optionString); } + else if(commandName == "otu.association") { pipecommand = new OTUAssociationCommand(optionString); } + else if(commandName == "sort.seqs") { pipecommand = new SortSeqsCommand(optionString); } + else if(commandName == "classify.tree") { pipecommand = new ClassifyTreeCommand(optionString); } else { pipecommand = new NoCommand(optionString); } return pipecommand; @@ -554,10 +606,10 @@ 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(); } - if(commandName == "cluster") { shellcommand = new ClusterCommand(); } + 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(); } else if(commandName == "unique.seqs") { shellcommand = new DeconvoluteCommand(); } else if(commandName == "parsimony") { shellcommand = new ParsimonyCommand(); } else if(commandName == "help") { shellcommand = new HelpCommand(); } @@ -592,7 +644,7 @@ Command* CommandFactory::getCommand(string commandName){ else if(commandName == "reverse.seqs") { shellcommand = new ReverseSeqsCommand(); } 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 == "shhh.flows") { shellcommand = new ShhherCommand(); } else if(commandName == "list.seqs") { shellcommand = new ListSeqsCommand(); } else if(commandName == "get.seqs") { shellcommand = new GetSeqsCommand(); } else if(commandName == "remove.seqs") { shellcommand = new RemoveSeqsCommand(); } @@ -606,6 +658,7 @@ 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(); } @@ -659,6 +712,18 @@ Command* CommandFactory::getCommand(string commandName){ 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 if(commandName == "count.seqs") { 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(); } + else if(commandName == "summary.qual") { shellcommand = new SummaryQualCommand(); } + else if(commandName == "chimera.perseus") { shellcommand = new ChimeraPerseusCommand(); } + else if(commandName == "shhh.seqs") { shellcommand = new ShhhSeqsCommand(); } + else if(commandName == "otu.association") { shellcommand = new OTUAssociationCommand(); } + else if(commandName == "sort.seqs") { shellcommand = new SortSeqsCommand(); } + else if(commandName == "classify.tree") { shellcommand = new ClassifyTreeCommand(); } else { shellcommand = new NoCommand(); } return shellcommand; @@ -684,7 +749,7 @@ Command* CommandFactory::getCommand(){ exit(1); } } -/***********************************************************************/ +***********************************************************************/ bool CommandFactory::isValidCommand(string command) { try {