#include "collectsharedcommand.h"
#include "getgroupcommand.h"
#include "getlabelcommand.h"
-#include "getlinecommand.h"
#include "rarefactcommand.h"
#include "summarycommand.h"
#include "summarysharedcommand.h"
#include "getoturepcommand.h"
#include "treegroupscommand.h"
#include "bootstrapsharedcommand.h"
-//#include "concensuscommand.h"
+//#include "consensuscommand.h"
#include "distancecommand.h"
#include "aligncommand.h"
#include "matrixoutputcommand.h"
#include "reversecommand.h"
#include "trimseqscommand.h"
#include "mergefilecommand.h"
+#include "chimeraseqscommand.h"
+#include "listseqscommand.h"
+#include "getseqscommand.h"
+#include "removeseqscommand.h"
+#include "systemcommand.h"
+#include "secondarystructurecommand.h"
+#include "getsharedotucommand.h"
+#include "getlistcountcommand.h"
+#include "hclustercommand.h"
+#include "classifyseqscommand.h"
+#include "phylotypecommand.h"
+#include "mgclustercommand.h"
+#include "preclustercommand.h"
+#include "pcacommand.h"
+#include "otuhierarchycommand.h"
+#include "setdircommand.h"
+/*******************************************************/
+
+/******************************************************/
+CommandFactory* CommandFactory::getInstance() {
+ if( _uniqueInstance == 0) {
+ _uniqueInstance = new CommandFactory();
+ }
+ return _uniqueInstance;
+}
/***********************************************************/
/***********************************************************/
string s = "";
command = new NoCommand(s);
+ outputDir = ""; inputDir = "";
//initialize list of valid commands
commands["read.dist"] = "read.dist";
commands["venn"] = "venn";
commands["get.group"] = "get.group";
commands["get.label"] = "get.label";
- commands["get.line"] = "get.line";
commands["get.sabund"] = "get.sabund";
commands["get.rabund"] = "get.rabund";
commands["bootstrap.shared"] = "bootstrap.shared";
- //commands["concensus"] = "concensus";
+ //commands["consensus"] = "consensus";
commands["help"] = "help";
commands["filter.seqs"] = "filter.seqs";
commands["align.seqs"] = "align.seqs";
commands["screen.seqs"] = "screen.seqs";
commands["reverse.seqs"] = "reverse.seqs";
commands["trim.seqs"] = "trim.seqs";
+ commands["chimera.seqs"] = "chimera.seqs";
+ commands["list.seqs"] = "list.seqs";
+ commands["get.seqs"] = "get.seqs";
+ commands["remove.seqs"] = "get.seqs";
+ commands["system"] = "system";
+ commands["align.check"] = "align.check";
+ commands["get.sharedseqs"] = "get.sharedseqs";
+ commands["get.otulist"] = "get.otulist";
commands["quit"] = "quit";
-
+ commands["hcluster"] = "hcluster";
+ commands["classify.seqs"] = "classify.seqs";
+ commands["phylotype"] = "phylotype";
+ commands["mgcluster"] = "mgcluster";
+ commands["pre.cluster"] = "pre.cluster";
+ commands["pca"] = "pca";
+ commands["otu.hierarchy"] = "otu.hierarchy";
+ commands["set.dir"] = "set.dir";
}
/***********************************************************/
/***********************************************************/
CommandFactory::~CommandFactory(){
+ _uniqueInstance = 0;
delete command;
}
Command* CommandFactory::getCommand(string commandName, string optionString){
try {
delete command; //delete the old command
-
+
+ //user has opted to redirect output from dir where input files are located to some other place
+ if (outputDir != "") {
+ if (optionString != "") { optionString += ", outputdir=" + outputDir; }
+ else { optionString += "outputdir=" + outputDir; }
+ }
+
+ //user has opted to redirect input from dir where mothur.exe is located to some other place
+ if (inputDir != "") {
+ if (optionString != "") { optionString += ", inputdir=" + inputDir; }
+ 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 == "unifrac.unweighted") { command = new UnifracUnweightedCommand(optionString); }
else if(commandName == "get.group") { command = new GetgroupCommand(optionString); }
else if(commandName == "get.label") { command = new GetlabelCommand(optionString); }
- else if(commandName == "get.line") { command = new GetlineCommand(optionString); }
else if(commandName == "get.sabund") { command = new GetSAbundCommand(optionString); }
else if(commandName == "get.rabund") { command = new GetRAbundCommand(optionString); }
else if(commandName == "libshuff") { command = new LibShuffCommand(optionString); }
else if(commandName == "tree.shared") { command = new TreeGroupCommand(optionString); }
else if(commandName == "dist.shared") { command = new MatrixOutputCommand(optionString); }
else if(commandName == "bootstrap.shared") { command = new BootSharedCommand(optionString); }
- //else if(commandName == "concensus") { command = new ConcensusCommand(optionString); }
+ //else if(commandName == "consensus") { command = new ConcensusCommand(optionString); }
else if(commandName == "dist.seqs") { command = new DistanceCommand(optionString); }
else if(commandName == "align.seqs") { command = new AlignCommand(optionString); }
else if(commandName == "summary.seqs") { command = new SeqSummaryCommand(optionString); }
else if(commandName == "screen.seqs") { command = new ScreenSeqsCommand(optionString); }
else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(optionString); }
else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(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); }
else if(commandName == "merge.files") { command = new MergeFileCommand(optionString); }
+ else if(commandName == "system") { command = new SystemCommand(optionString); }
+ else if(commandName == "align.check") { command = new AlignCheckCommand(optionString); }
+ else if(commandName == "get.sharedseqs") { command = new GetSharedOTUCommand(optionString); }
+ else if(commandName == "get.otulist") { command = new GetListCountCommand(optionString); }
+ else if(commandName == "hcluster") { command = new HClusterCommand(optionString); }
+ else if(commandName == "classify.seqs") { command = new ClassifySeqsCommand(optionString); }
+ else if(commandName == "phylotype") { command = new PhylotypeCommand(optionString); }
+ else if(commandName == "mgcluster") { command = new MGClusterCommand(optionString); }
+ else if(commandName == "pre.cluster") { command = new PreClusterCommand(optionString); }
+ else if(commandName == "pca") { command = new PCACommand(optionString); }
+ else if(commandName == "otu.hierarchy") { command = new OtuHierarchyCommand(optionString); }
+ else if(commandName == "set.dir") { command = new SetDirectoryCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
exit(1);
}
}
+/***********************************************************/
+//This function is used to interrupt a command
+Command* CommandFactory::getCommand(){
+ try {
+ delete command; //delete the old command
+ string s = "";
+ command = new NoCommand(s);
+
+ return command;
+ }
+ catch(exception& e) {
+ errorOut(e, "CommandFactory", "getCommand");
+ exit(1);
+ }
+}
/***********************************************************************/
bool CommandFactory::isValidCommand(string command) {
try {
projects / mothur.git / blobdiff