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/*
* 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,true); parameters.push_back(pprocessors);
CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pflow);
CommandParameter pfile("file", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfile);
CommandParameter psample("sample", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psample);
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 pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pconstaxonomy);
CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcontigsreport);
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 pclr("clr", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pclr);
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 pcurrent("current", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcurrent);
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 pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
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: current, clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, clr, fasta, qfile, sff, oligos, accnos, biom, count, summary, file, contigsreport, constaxonomy, taxonomy and sample.\n";
helpString += "The current parameter is used to input the output file from get.current. This function is intended to allow you to input filenames from previous instances on mothur. NOTE: If you have a current file set in the file *.current_files.summary file, and also set a value for that file type, the value set takes precedence. For example, if you run set.current(current=current_files.summary, fasta=abrecovery.fasta) and your have fasta=final.fasta in the *.current_files.summary file the current fasta file will be set to abrecovery.fasta.\n";
helpString += "The clear parameter 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);
}
}
//**********************************************************************************************************************
string SetCurrentCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "summary") { pattern = "[filename],current_files.summary"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "SetCurrentCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
SetCurrentCommand::SetCurrentCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
currentFile = validParameter.validFile(parameters, "current");
if (currentFile == "not open") { m->mothurOut("Ignoring: " + parameters["current"]); m->mothurOutEndLine(); currentFile = ""; }
else if (currentFile == "not found") { currentFile = ""; }
if (currentFile != "") { readCurrentFiles(); } //setting variables overwrites the settings in the file.
//check for parameters
phylipfile = validParameter.validFile(parameters, "phylip");
if (phylipfile == "not open") { m->mothurOut("Ignoring: " + parameters["phylip"]); m->mothurOutEndLine(); phylipfile = ""; }
else if (phylipfile == "not found") { phylipfile = ""; }
if (phylipfile != "") { current->setPhylipFile(phylipfile); }
columnfile = validParameter.validFile(parameters, "column");
if (columnfile == "not open") { m->mothurOut("Ignoring: " + parameters["column"]); m->mothurOutEndLine(); columnfile = ""; }
else if (columnfile == "not found") { columnfile = ""; }
if (columnfile != "") { current->setColumnFile(columnfile); }
listfile = validParameter.validFile(parameters, "list");
if (listfile == "not open") { m->mothurOut("Ignoring: " + parameters["list"]); m->mothurOutEndLine(); listfile = ""; }
else if (listfile == "not found") { listfile = ""; }
if (listfile != "") { current->setListFile(listfile); }
rabundfile = validParameter.validFile(parameters, "rabund");
if (rabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["rabund"]); m->mothurOutEndLine(); rabundfile = ""; }
else if (rabundfile == "not found") { rabundfile = ""; }
if (rabundfile != "") { current->setRabundFile(rabundfile); }
sabundfile = validParameter.validFile(parameters, "sabund");
if (sabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["sabund"]); m->mothurOutEndLine(); sabundfile = ""; }
else if (sabundfile == "not found") { sabundfile = ""; }
if (sabundfile != "") { current->setSabundFile(sabundfile); }
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { m->mothurOut("Ignoring: " + parameters["name"]); m->mothurOutEndLine(); namefile = ""; }
else if (namefile == "not found") { namefile = ""; }
if (namefile != "") { current->setNameFile(namefile); }
groupfile = validParameter.validFile(parameters, "group");
if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
else if (groupfile == "not found") { groupfile = ""; }
if (groupfile != "") { current->setGroupFile(groupfile); }
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { m->mothurOut("Ignoring: " + parameters["count"]); m->mothurOutEndLine(); countfile = ""; }
else if (countfile == "not found") { countfile = ""; }
if (countfile != "") { current->setCountFile(countfile); }
designfile = validParameter.validFile(parameters, "design");
if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
else if (designfile == "not found") { designfile = ""; }
if (designfile != "") { current->setDesignFile(designfile); }
orderfile = validParameter.validFile(parameters, "order");
if (orderfile == "not open") { m->mothurOut("Ignoring: " + parameters["order"]); m->mothurOutEndLine(); orderfile = ""; }
else if (orderfile == "not found") { orderfile = ""; }
if (orderfile != "") { current->setOrderFile(orderfile); }
treefile = validParameter.validFile(parameters, "tree");
if (treefile == "not open") { m->mothurOut("Ignoring: " + parameters["tree"]); m->mothurOutEndLine(); treefile = ""; }
else if (treefile == "not found") { treefile = ""; }
if (treefile != "") { current->setTreeFile(treefile); }
sharedfile = validParameter.validFile(parameters, "shared");
if (sharedfile == "not open") { m->mothurOut("Ignoring: " + parameters["shared"]); m->mothurOutEndLine(); sharedfile = ""; }
else if (sharedfile == "not found") { sharedfile = ""; }
if (sharedfile != "") { current->setSharedFile(sharedfile); }
clrfile = validParameter.validFile(parameters, "clr");
if (clrfile == "not open") { m->mothurOut("Ignoring: " + parameters["clr"]); m->mothurOutEndLine(); clrfile = ""; }
else if (clrfile == "not found") { clrfile = ""; }
if (clrfile != "") { current->setCLRFile(clrfile); }
ordergroupfile = validParameter.validFile(parameters, "ordergroup");
if (ordergroupfile == "not open") { m->mothurOut("Ignoring: " + parameters["ordergroup"]); m->mothurOutEndLine(); ordergroupfile = ""; }
else if (ordergroupfile == "not found") { ordergroupfile = ""; }
if (ordergroupfile != "") { current->setOrderGroupFile(ordergroupfile); }
relabundfile = validParameter.validFile(parameters, "relabund");
if (relabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["relabund"]); m->mothurOutEndLine(); relabundfile = ""; }
else if (relabundfile == "not found") { relabundfile = ""; }
if (relabundfile != "") { current->setRelAbundFile(relabundfile); }
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not open") { m->mothurOut("Ignoring: " + parameters["fasta"]); m->mothurOutEndLine(); fastafile = ""; }
else if (fastafile == "not found") { fastafile = ""; }
if (fastafile != "") { current->setFastaFile(fastafile); }
qualfile = validParameter.validFile(parameters, "qfile");
if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLine(); qualfile = ""; }
else if (qualfile == "not found") { qualfile = ""; }
if (qualfile != "") { current->setQualFile(qualfile); }
sfffile = validParameter.validFile(parameters, "sff");
if (sfffile == "not open") { m->mothurOut("Ignoring: " + parameters["sff"]); m->mothurOutEndLine(); sfffile = ""; }
else if (sfffile == "not found") { sfffile = ""; }
if (sfffile != "") { current->setSFFFile(sfffile); }
oligosfile = validParameter.validFile(parameters, "oligos");
if (oligosfile == "not open") { m->mothurOut("Ignoring: " + parameters["oligos"]); m->mothurOutEndLine(); oligosfile = ""; }
else if (oligosfile == "not found") { oligosfile = ""; }
if (oligosfile != "") { current->setOligosFile(oligosfile); }
accnosfile = validParameter.validFile(parameters, "accnos");
if (accnosfile == "not open") { m->mothurOut("Ignoring: " + parameters["accnos"]); m->mothurOutEndLine(); accnosfile = ""; }
else if (accnosfile == "not found") { accnosfile = ""; }
if (accnosfile != "") { current->setAccnosFile(accnosfile); }
taxonomyfile = validParameter.validFile(parameters, "taxonomy");
if (taxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["taxonomy"]); m->mothurOutEndLine(); taxonomyfile = ""; }
else if (taxonomyfile == "not found") { taxonomyfile = ""; }
if (taxonomyfile != "") { current->setTaxonomyFile(taxonomyfile); }
contigsreportfile = validParameter.validFile(parameters, "contigsreport");
if (contigsreportfile == "not open") { m->mothurOut("Ignoring: " + parameters["contigsreport"]); m->mothurOutEndLine(); contigsreportfile = ""; }
else if (contigsreportfile == "not found") { contigsreportfile = ""; }
if (contigsreportfile != "") { current->setContigsReportFile(contigsreportfile); }
constaxonomyfile = validParameter.validFile(parameters, "constaxonomy");
if (constaxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["constaxonomy"]); m->mothurOutEndLine(); constaxonomyfile = ""; }
else if (constaxonomyfile == "not found") { constaxonomyfile = ""; }
if (constaxonomyfile != "") { current->setConsTaxonomyFile(constaxonomyfile); }
flowfile = validParameter.validFile(parameters, "flow");
if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; }
else if (flowfile == "not found") { flowfile = ""; }
if (flowfile != "") { current->setFlowFile(flowfile); }
biomfile = validParameter.validFile(parameters, "biom");
if (biomfile == "not open") { m->mothurOut("Ignoring: " + parameters["biom"]); m->mothurOutEndLine(); biomfile = ""; }
else if (biomfile == "not found") { biomfile = ""; }
if (biomfile != "") { current->setBiomFile(biomfile); }
summaryfile = validParameter.validFile(parameters, "summary");
if (summaryfile == "not open") { m->mothurOut("Ignoring: " + parameters["summary"]); m->mothurOutEndLine(); summaryfile = ""; }
else if (summaryfile == "not found") { summaryfile = ""; }
if (summaryfile != "") { current->setSummaryFile(summaryfile); }
filefile = validParameter.validFile(parameters, "file");
if (filefile == "not open") { m->mothurOut("Ignoring: " + parameters["file"]); m->mothurOutEndLine(); filefile = ""; }
else if (filefile == "not found") { filefile = ""; }
if (filefile != "") { current->setFileFile(filefile); }
samplefile = validParameter.validFile(parameters, "sample");
if (samplefile == "not open") { m->mothurOut("Ignoring: " + parameters["sample"]); m->mothurOutEndLine(); samplefile = ""; }
else if (samplefile == "not found") { samplefile = ""; }
if (samplefile != "") { current->setSampleFile(samplefile); }
string temp = validParameter.valid(parameters, "processors");
if (temp == "not found"){ temp = current->getProcessors(); }
current->setProcessors(temp);
clearTypes = validParameter.valid(parameters, "clear");
if (clearTypes == "not found") { clearTypes = ""; }
else { util.splitAtDash(clearTypes, types); }
}
}
catch(exception& e) {
m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
exit(1);
}
}
//**********************************************************************************************************************
int SetCurrentCommand::execute(){
try {
if (abort) { 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->getControl_pressed()) { break; }
//look for file types
if (types[i] == "fasta") {
current->setFastaFile("");
}else if (types[i] == "qfile") {
current->setQualFile("");
}else if (types[i] == "phylip") {
current->setPhylipFile("");
}else if (types[i] == "column") {
current->setColumnFile("");
}else if (types[i] == "list") {
current->setListFile("");
}else if (types[i] == "rabund") {
current->setRabundFile("");
}else if (types[i] == "sabund") {
current->setSabundFile("");
}else if (types[i] == "name") {
current->setNameFile("");
}else if (types[i] == "group") {
current->setGroupFile("");
}else if (types[i] == "order") {
current->setOrderFile("");
}else if (types[i] == "ordergroup") {
current->setOrderGroupFile("");
}else if (types[i] == "tree") {
current->setTreeFile("");
}else if (types[i] == "shared") {
current->setSharedFile("");
}else if (types[i] == "relabund") {
current->setRelAbundFile("");
}else if (types[i] == "clr") {
current->setCLRFile("");
}else if (types[i] == "design") {
current->setDesignFile("");
}else if (types[i] == "sff") {
current->setSFFFile("");
}else if (types[i] == "oligos") {
current->setOligosFile("");
}else if (types[i] == "accnos") {
current->setAccnosFile("");
}else if (types[i] == "taxonomy") {
current->setTaxonomyFile("");
}else if (types[i] == "constaxonomy") {
current->setConsTaxonomyFile("");
}else if (types[i] == "contigsreport") {
current->setContigsReportFile("");
}else if (types[i] == "flow") {
current->setFlowFile("");
}else if (types[i] == "biom") {
current->setBiomFile("");
}else if (types[i] == "count") {
current->setCountFile("");
}else if (types[i] == "summary") {
current->setSummaryFile("");
}else if (types[i] == "file") {
current->setFileFile("");
}else if (types[i] == "sample") {
current->setSampleFile("");
}else if (types[i] == "processors") {
current->setProcessors("1");
}else if (types[i] == "all") {
current->clearCurrentFiles();
}else {
m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i] + "\n");
}
}
}
m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:\n");
if (current->hasCurrentFiles()) {
map<string, string> variables;
variables["[filename]"] = util.getFullPathName(outputdir);
string filename = getOutputFileName("summary", variables);
current->printCurrentFiles(filename);
outputNames.push_back(filename); outputTypes["summary"].push_back(filename);
m->mothurOutEndLine();
m->mothurOut("Output File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SetCurrentCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int SetCurrentCommand::readCurrentFiles(){
try{
ifstream in; util.openInputFile(currentFile, in);
while(!in.eof()) {
if (m->getControl_pressed()) { break; }
string line = util.getline(in); gobble(in);
vector<string> pieces;
util.splitAtChar(line, pieces, '=');
if (pieces.size() != 2) { m->mothurOut("[ERROR]: " + util.getStringFromVector(pieces, ",") + " line is not in the correct format. Did you edit the file? Mothur expects tag=filename. Example: fasta=final.fasta\n"); m->setControl_pressed(true); }
else{
//look for file types
if (pieces[0] == "fasta") {
current->setFastaFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "qfile") {
current->setQualFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "phylip") {
current->setPhylipFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "column") {
current->setColumnFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "list") {
current->setListFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "rabund") {
current->setRabundFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "sabund") {
current->setSabundFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "name") {
current->setNameFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "group") {
current->setGroupFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "order") {
current->setOrderFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "ordergroup") {
current->setOrderGroupFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "tree") {
current->setTreeFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "shared") {
current->setSharedFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "relabund") {
current->setRelAbundFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "clr") {
current->setCLRFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "design") {
current->setDesignFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "sff") {
current->setSFFFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "oligos") {
current->setOligosFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "accnos") {
current->setAccnosFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "taxonomy") {
current->setTaxonomyFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "constaxonomy") {
current->setConsTaxonomyFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "contigsreport") {
current->setContigsReportFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "flow") {
current->setFlowFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "biom") {
current->setBiomFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "count") {
current->setCountFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "summary") {
current->setSummaryFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "file") {
current->setFileFile(util.getFullPathName(pieces[1]));
}else if (pieces[0] == "processors") {
current->setProcessors(pieces[1]);
}else {
m->mothurOut("[ERROR]: mothur does not save a current file for " + util.getFullPathName(pieces[1])); m->mothurOutEndLine();
}
}
}
in.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SetCurrentCommand", "readCurrentFiles");
exit(1);
}
}
//**********************************************************************************************************************
|
