#include "readtreecommand.h"
#include "readotucommand.h"
#include "clustercommand.h"
-#include "parselistcommand.h"
#include "collectcommand.h"
#include "collectsharedcommand.h"
#include "getgroupcommand.h"
#include "getlabelcommand.h"
-#include "getlinecommand.h"
#include "rarefactcommand.h"
#include "summarycommand.h"
#include "summarysharedcommand.h"
#include "heatmapcommand.h"
#include "heatmapsimcommand.h"
#include "filterseqscommand.h"
-#include "mothur.h"
#include "venncommand.h"
#include "nocommands.h"
#include "binsequencecommand.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 "screenseqscommand.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;
+}
/***********************************************************/
/***********************************************************/
CommandFactory::CommandFactory(){
string s = "";
command = new NoCommand(s);
+
+ outputDir = ""; inputDir = "";
+
+ //initialize list of valid commands
+ commands["read.dist"] = "read.dist";
+ commands["read.otu"] = "read.otu";
+ commands["read.tree"] = "read.tree";
+ commands["bin.seqs"] = "bin.seqs";
+ commands["get.oturep"] = "get.oturep";
+ commands["cluster"] = "cluster";
+ commands["unique.seqs"] = "unique.seqs";
+ commands["dist.seqs"] = "dist.seqs";
+ commands["dist.shared"] = "dist.shared";
+ commands["collect.single"] = "collect.single";
+ commands["collect.shared"] = "collect.shared";
+ commands["rarefaction.single"] = "rarefaction.single";
+ commands["rarefaction.shared"] = "rarefaction.shared";
+ commands["summary.single"] = "summary.single";
+ commands["summary.shared"] = "summary.shared";
+ commands["parsimony"] = "parsimony";
+ commands["unifrac.weighted"] = "unifrac.weighted";
+ commands["unifrac.unweighted"] = "unifrac.unweighted";
+ commands["libshuff"] = "libshuff";
+ commands["tree.shared"] = "tree.shared";
+ commands["heatmap.bin"] = "heatmap.bin";
+ commands["heatmap.sim"] = "heatmap.sim";
+ commands["venn"] = "venn";
+ commands["get.group"] = "get.group";
+ commands["get.label"] = "get.label";
+ commands["get.sabund"] = "get.sabund";
+ commands["get.rabund"] = "get.rabund";
+ commands["bootstrap.shared"] = "bootstrap.shared";
+ //commands["consensus"] = "consensus";
+ commands["help"] = "help";
+ commands["filter.seqs"] = "filter.seqs";
+ commands["align.seqs"] = "align.seqs";
+ commands["summary.seqs"] = "summary.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["pcoa"] = "pcoa";
+ 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 == "pcoa") { 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;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CommandFactory class Function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "CommandFactory", "getCommand");
+ 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);
}
- catch(...) {
- cout << "An unknown error has occurred in the CommandFactory class function getCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************************/
+bool CommandFactory::isValidCommand(string command) {
+ try {
+
+ //is the command in the map
+ if ((commands.find(command)) != (commands.end())) {
+ return true;
+ }else{
+ mothurOut(command + " is not a valid command in Mothur. Valid commands are ");
+ for (it = commands.begin(); it != commands.end(); it++) {
+ mothurOut(it->first + ", ");
+ }
+ mothurOutEndLine();
+ return false;
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "CommandFactory", "isValidCommand");
exit(1);
}
+}
+/***********************************************************************/
+void CommandFactory::printCommands(ostream& out) {
+ try {
+ out << "Valid commands are ";
+ for (it = commands.begin(); it != commands.end(); it++) {
+ out << it->first << ", ";
+ }
+ out << endl;
+ }
+ catch(exception& e) {
+ errorOut(e, "CommandFactory", "printCommands");
+ exit(1);
+ }
}
-/***********************************************************/
+/***********************************************************************/
+
+
+
projects / mothur.git / blobdiff