#include "setcurrentcommand.h"
//**********************************************************************************************************************
-vector<string> SetCurrentCommand::getValidParameters(){
+vector<string> SetCurrentCommand::setParameters(){
try {
- string Array[] = {"outputdir","inputdir","clear", "phylip", "column", "list","rabund","sabund","name","group",
- "design","order","tree","shared","ordergroup","relabund","fasta","qfile","sff","oligos","accnos","taxonomy"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pflow);
+ CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pbiom);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pphylip);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcolumn);
+ CommandParameter psummary("summary", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psummary);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pqfile);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psabund);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pdesign);
+ CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(porder);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptree);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pshared);
+ CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pordergroup);
+ CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcount);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prelabund);
+ CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psff);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
+ CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "SetCurrentCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-SetCurrentCommand::SetCurrentCommand(){
- try {
- abort = true; calledHelp = true;
- }
- catch(exception& e) {
- m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
+ m->errorOut(e, "SetCurrentCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SetCurrentCommand::getRequiredParameters(){
+string SetCurrentCommand::getHelpString(){
try {
- vector<string> myArray;
- return myArray;
+ string helpString = "";
+ helpString += "The set.current command allows you to set the current files saved by mothur.\n";
+ helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom, count, summary and taxonomy.\n";
+ helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
+ helpString += "The set.current command should be in the following format: \n";
+ helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "SetCurrentCommand", "getRequiredParameters");
+ m->errorOut(e, "SetCurrentCommand", "getHelpString");
exit(1);
}
}
+
+
//**********************************************************************************************************************
-vector<string> SetCurrentCommand::getRequiredFiles(){
+SetCurrentCommand::SetCurrentCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
}
catch(exception& e) {
- m->errorOut(e, "SetCurrentCommand", "getRequiredFiles");
+ m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
exit(1);
}
}
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
//valid paramters for this command
- string Array[] = {"outputdir","inputdir","clear", "phylip", "column", "list","rabund","sabund","name","group",
- "design","order","tree","shared","ordergroup","relabund","fasta","qfile","sff","oligos","accnos","taxonomy"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
if (path == "") { parameters["ordergroup"] = inputDir + it->second; }
}
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
+
it = parameters.find("relabund");
//user has given a template file
if(it != parameters.end()){
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
}
+
+ it = parameters.find("flow");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["flow"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("biom");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["biom"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("summary");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["summary"] = inputDir + it->second; }
+ }
}
//check for parameters
if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
else if (groupfile == "not found") { groupfile = ""; }
if (groupfile != "") { m->setGroupFile(groupfile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { m->mothurOut("Ignoring: " + parameters["count"]); m->mothurOutEndLine(); countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ if (countfile != "") { m->setCountTableFile(countfile); }
designfile = validParameter.validFile(parameters, "design", true);
if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
else if (taxonomyfile == "not found") { taxonomyfile = ""; }
if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
+ flowfile = validParameter.validFile(parameters, "flow", true);
+ if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; }
+ else if (flowfile == "not found") { flowfile = ""; }
+ if (flowfile != "") { m->setFlowFile(flowfile); }
+
+ biomfile = validParameter.validFile(parameters, "biom", true);
+ if (biomfile == "not open") { m->mothurOut("Ignoring: " + parameters["biom"]); m->mothurOutEndLine(); biomfile = ""; }
+ else if (biomfile == "not found") { biomfile = ""; }
+ if (biomfile != "") { m->setBiomFile(biomfile); }
+
+ summaryfile = validParameter.validFile(parameters, "summary", true);
+ if (summaryfile == "not open") { m->mothurOut("Ignoring: " + parameters["summary"]); m->mothurOutEndLine(); summaryfile = ""; }
+ else if (summaryfile == "not found") { summaryfile = ""; }
+ if (summaryfile != "") { m->setSummaryFile(summaryfile); }
+
+
+ processors = validParameter.validFile(parameters, "processors", false);
+ if (processors == "not found") { processors = "1"; }
+ if (processors != "") { m->setProcessors(processors); }
+
clearTypes = validParameter.validFile(parameters, "clear", false);
if (clearTypes == "not found") { clearTypes = ""; }
else { m->splitAtDash(clearTypes, types); }
}
//**********************************************************************************************************************
-void SetCurrentCommand::help(){
- try {
- m->mothurOut("The set.current command allows you to set the current files saved by mothur.\n");
- m->mothurOut("The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, taxonomy.\n");
- m->mothurOut("The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n");
- m->mothurOut("The set.current command should be in the following format: \n");
- m->mothurOut("set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "SetCurrentCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-SetCurrentCommand::~SetCurrentCommand(){}
-//**********************************************************************************************************************
-
int SetCurrentCommand::execute(){
try {
m->setAccnosFile("");
}else if (types[i] == "taxonomy") {
m->setTaxonomyFile("");
+ }else if (types[i] == "flow") {
+ m->setFlowFile("");
+ }else if (types[i] == "biom") {
+ m->setBiomFile("");
+ }else if (types[i] == "count") {
+ m->setCountTableFile("");
+ }else if (types[i] == "summary") {
+ m->setSummaryFile("");
+ }else if (types[i] == "processors") {
+ m->setProcessors("1");
}else if (types[i] == "all") {
m->clearCurrentFiles();
}else {
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