+++ /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::setParameters(){
- try {
-
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); 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 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 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", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string SetCurrentCommand::getHelpString(){
- try {
- 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 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", "getHelpString");
- exit(1);
- }
-}
-
-
-//**********************************************************************************************************************
-SetCurrentCommand::SetCurrentCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- }
- catch(exception& e) {
- m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
- 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 if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- //valid paramters for this command
- vector<string> myArray = setParameters();
-
- 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; }
- }
-
- 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; }
- }
- }
-
- //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); }
-
- 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); }
-
- 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); }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-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] == "flow") {
- m->setFlowFile("");
- }else if (types[i] == "biom") {
- m->setBiomFile("");
- }else if (types[i] == "processors") {
- m->setProcessors("1");
- }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);
- }
-}
-
-//**********************************************************************************************************************
-
-
-