--- /dev/null
+/*
+ * setcurrentcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 3/16/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "setcurrentcommand.h"
+
+//**********************************************************************************************************************
+vector<string> SetCurrentCommand::getValidParameters(){
+ 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)));
+ 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");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SetCurrentCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SetCurrentCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SetCurrentCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SetCurrentCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SetCurrentCommand::SetCurrentCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); 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)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("phylip");
+ //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["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("column");
+ //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["column"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("fasta");
+ //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["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //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["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("rabund");
+ //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["rabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("sabund");
+ //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["sabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //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["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("design");
+ //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["design"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("order");
+ //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["order"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("tree");
+ //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["tree"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("shared");
+ //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["shared"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("ordergroup");
+ //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["ordergroup"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("relabund");
+ //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["relabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("fasta");
+ //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["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("qfile");
+ //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["qfile"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("sff");
+ //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["sff"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("oligos");
+ //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["oligos"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("accnos");
+ //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["accnos"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("taxonomy");
+ //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["taxonomy"] = inputDir + it->second; }
+ }
+ }
+
+ //check for parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { m->mothurOut("Ignoring: " + parameters["phylip"]); m->mothurOutEndLine(); phylipfile = ""; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ if (phylipfile != "") { m->setPhylipFile(phylipfile); }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not open") { m->mothurOut("Ignoring: " + parameters["column"]); m->mothurOutEndLine(); columnfile = ""; }
+ else if (columnfile == "not found") { columnfile = ""; }
+ if (columnfile != "") { m->setColumnFile(columnfile); }
+
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { m->mothurOut("Ignoring: " + parameters["list"]); m->mothurOutEndLine(); listfile = ""; }
+ else if (listfile == "not found") { listfile = ""; }
+ if (listfile != "") { m->setListFile(listfile); }
+
+ rabundfile = validParameter.validFile(parameters, "rabund", true);
+ if (rabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["rabund"]); m->mothurOutEndLine(); rabundfile = ""; }
+ else if (rabundfile == "not found") { rabundfile = ""; }
+ if (rabundfile != "") { m->setRabundFile(rabundfile); }
+
+ sabundfile = validParameter.validFile(parameters, "sabund", true);
+ if (sabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["sabund"]); m->mothurOutEndLine(); sabundfile = ""; }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+ if (sabundfile != "") { m->setSabundFile(sabundfile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { m->mothurOut("Ignoring: " + parameters["name"]); m->mothurOutEndLine(); namefile = ""; }
+ else if (namefile == "not found") { namefile = ""; }
+ if (namefile != "") { m->setNameFile(namefile); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ if (groupfile != "") { m->setGroupFile(groupfile); }
+
+ designfile = validParameter.validFile(parameters, "design", true);
+ if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
+ else if (designfile == "not found") { designfile = ""; }
+ if (designfile != "") { m->setDesignFile(designfile); }
+
+ orderfile = validParameter.validFile(parameters, "order", true);
+ if (orderfile == "not open") { m->mothurOut("Ignoring: " + parameters["order"]); m->mothurOutEndLine(); orderfile = ""; }
+ else if (orderfile == "not found") { orderfile = ""; }
+ if (orderfile != "") { m->setOrderFile(orderfile); }
+
+ treefile = validParameter.validFile(parameters, "tree", true);
+ if (treefile == "not open") { m->mothurOut("Ignoring: " + parameters["tree"]); m->mothurOutEndLine(); treefile = ""; }
+ else if (treefile == "not found") { treefile = ""; }
+ if (treefile != "") { m->setTreeFile(treefile); }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { m->mothurOut("Ignoring: " + parameters["shared"]); m->mothurOutEndLine(); sharedfile = ""; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ if (sharedfile != "") { m->setSharedFile(sharedfile); }
+
+ ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
+ if (ordergroupfile == "not open") { m->mothurOut("Ignoring: " + parameters["ordergroup"]); m->mothurOutEndLine(); ordergroupfile = ""; }
+ else if (ordergroupfile == "not found") { ordergroupfile = ""; }
+ if (ordergroupfile != "") { m->setOrderGroupFile(ordergroupfile); }
+
+ relabundfile = validParameter.validFile(parameters, "relabund", true);
+ if (relabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["relabund"]); m->mothurOutEndLine(); relabundfile = ""; }
+ else if (relabundfile == "not found") { relabundfile = ""; }
+ if (relabundfile != "") { m->setRelAbundFile(relabundfile); }
+
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { m->mothurOut("Ignoring: " + parameters["fasta"]); m->mothurOutEndLine(); fastafile = ""; }
+ else if (fastafile == "not found") { fastafile = ""; }
+ if (fastafile != "") { m->setFastaFile(fastafile); }
+
+ qualfile = validParameter.validFile(parameters, "qfile", true);
+ if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLine(); qualfile = ""; }
+ else if (qualfile == "not found") { qualfile = ""; }
+ if (qualfile != "") { m->setQualFile(qualfile); }
+
+ sfffile = validParameter.validFile(parameters, "sff", true);
+ if (sfffile == "not open") { m->mothurOut("Ignoring: " + parameters["sff"]); m->mothurOutEndLine(); sfffile = ""; }
+ else if (sfffile == "not found") { sfffile = ""; }
+ if (sfffile != "") { m->setSFFFile(sfffile); }
+
+ oligosfile = validParameter.validFile(parameters, "oligos", true);
+ if (oligosfile == "not open") { m->mothurOut("Ignoring: " + parameters["oligos"]); m->mothurOutEndLine(); oligosfile = ""; }
+ else if (oligosfile == "not found") { oligosfile = ""; }
+ if (oligosfile != "") { m->setOligosFile(oligosfile); }
+
+ accnosfile = validParameter.validFile(parameters, "accnos", true);
+ if (accnosfile == "not open") { m->mothurOut("Ignoring: " + parameters["accnos"]); m->mothurOutEndLine(); accnosfile = ""; }
+ else if (accnosfile == "not found") { accnosfile = ""; }
+ if (accnosfile != "") { m->setAccnosFile(accnosfile); }
+
+ taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
+ if (taxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["taxonomy"]); m->mothurOutEndLine(); taxonomyfile = ""; }
+ else if (taxonomyfile == "not found") { taxonomyfile = ""; }
+ if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
+
+ clearTypes = validParameter.validFile(parameters, "clear", false);
+ if (clearTypes == "not found") { clearTypes = ""; }
+ else { m->splitAtDash(clearTypes, types); }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+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 {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //user wants to clear a type
+ if (types.size() != 0) {
+ for (int i = 0; i < types.size(); i++) {
+
+ if (m->control_pressed) { break; }
+
+ //look for file types
+ if (types[i] == "fasta") {
+ m->setFastaFile("");
+ }else if (types[i] == "qfile") {
+ m->setQualFile("");
+ }else if (types[i] == "phylip") {
+ m->setPhylipFile("");
+ }else if (types[i] == "column") {
+ m->setColumnFile("");
+ }else if (types[i] == "list") {
+ m->setListFile("");
+ }else if (types[i] == "rabund") {
+ m->setRabundFile("");
+ }else if (types[i] == "sabund") {
+ m->setSabundFile("");
+ }else if (types[i] == "name") {
+ m->setNameFile("");
+ }else if (types[i] == "group") {
+ m->setGroupFile("");
+ }else if (types[i] == "order") {
+ m->setOrderFile("");
+ }else if (types[i] == "ordergroup") {
+ m->setOrderGroupFile("");
+ }else if (types[i] == "tree") {
+ m->setTreeFile("");
+ }else if (types[i] == "shared") {
+ m->setSharedFile("");
+ }else if (types[i] == "relabund") {
+ m->setRelAbundFile("");
+ }else if (types[i] == "design") {
+ m->setDesignFile("");
+ }else if (types[i] == "sff") {
+ m->setSFFFile("");
+ }else if (types[i] == "oligos") {
+ m->setOligosFile("");
+ }else if (types[i] == "accnos") {
+ m->setAccnosFile("");
+ }else if (types[i] == "taxonomy") {
+ m->setTaxonomyFile("");
+ }else if (types[i] == "all") {
+ m->clearCurrentFiles();
+ }else {
+ m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
+ }
+ }
+ }
+
+ m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
+ m->printCurrentFiles();
+
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "SetCurrentCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
+
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