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//
// newcommandtemplate.cpp
// Mothur
//
// Created by Sarah Westcott on 5/3/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
//
#include "newcommandtemplate.h"
// Test Change.
//**********************************************************************************************************************
vector<string> NewCommand::setParameters(){
try {
//eaxamples of each type of parameter. more info on the types of parameters can be found in commandparameter.h
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pprocessors);
//files that have dependancies
CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","outputType",false,false); parameters.push_back(pphylip);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName","outputType",false,false); parameters.push_back(pname);
CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","outputType",false,false); parameters.push_back(pcolumn);
//files that do not have dependancies - fasta is set to not be required whereas shared is set to be required
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","outputType",false,false); parameters.push_back(pfasta);
CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","outputType",false,true); parameters.push_back(pshared);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
//choose more than one multiple options
CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "","",true,false); parameters.push_back(pcalc);
//choose only one multiple options
CommandParameter pdistance("distance", "Multiple", "column-lt-square", "column", "", "", "","",false,false); parameters.push_back(pdistance);
CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
//every command must have inputdir and outputdir. This allows mothur users to redirect input and output files.
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);
//set output file types
vector<string> tempOutNames;
outputTypes["fileType1"] = tempOutNames; //filetypes should be things like: shared, fasta, accnos...
outputTypes["fileType2"] = tempOutNames;
outputTypes["FileType3"] = tempOutNames;
//set abort and called Help
abort = false; calledHelp = false;
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, "NewCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string NewCommand::getHelpString(){
try {
string helpString = "";
helpString += "The new command allows you to ....\n";
helpString += "The new command parameters are: ....\n";
helpString += "The whatever parameter is used to ....\n";
helpString += "The new command should be in the following format: \n";
helpString += "new(...)\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "NewCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string NewCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fileType1") { pattern = "[filename],tag1"; }
else if (type == "fileType2") { pattern = "[filename],tag2"; }
else if (type == "fileType3") { pattern = "[filename],tag3"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "NewCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
NewCommand::NewCommand(string option) : Command() {
try {
////////////////////////////////////////////////////////
/////////////////// start leave alone block ////////////
////////////////////////////////////////////////////////
//allow user to run help
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 {
//valid paramters for this command
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
///variables for examples below that you will most likely want to put in the header for
//use by the other class functions.
string phylipfile, columnfile, namefile, fastafile, sharedfile, method, countfile;
int processors;
bool useTiming, allLines;
vector<string> Estimators, Groups;
set<string> labels;
//if allLines is used it should be initialized to 1 above.
//check for parameters
phylipfile = validParameter.validFile(parameters, "phylip");
if (phylipfile == "not open") { phylipfile = ""; abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
else { current->setPhylipFile(phylipfile); }
columnfile = validParameter.validFile(parameters, "column");
if (columnfile == "not open") { columnfile = ""; abort = true; }
else if (columnfile == "not found") { columnfile = ""; }
else { current->setColumnFile(columnfile); }
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { current->setNameFile(namefile); }
//get fastafile - it is not required
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not open") { fastafile = ""; abort=true; }
else if (fastafile == "not found") { fastafile = ""; }
if (fastafile != "") { current->setFastaFile(fastafile); }
if ((phylipfile == "") && (columnfile == "")) {
//is there are current file available for either of these?
//give priority to column, then phylip
columnfile = current->getColumnFile();
if (columnfile != "") { m->mothurOut("Using " + columnfile + " as input file for the column parameter.\n"); }
else {
phylipfile = current->getPhylipFile();
if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter.\n"); }
else {
m->mothurOut("No valid current files. You must provide a phylip or column file before you can use the cluster command.\n");
abort = true;
}
}
}
else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a cluster command you must enter ONLY ONE of the following: phylip or column.\n"); abort = true; }
if (columnfile != "") {
if (namefile == "") {
namefile = current->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter.\n"); }
else {
m->mothurOut("You need to provide a namefile if you are going to use the column format.\n");
abort = true;
}
}
}
//get shared file, it is required
sharedfile = validParameter.validFile(parameters, "shared");
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") {
//if there is a current shared file, use it
sharedfile = current->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter.\n"); }
else { m->mothurOut("You have no current sharedfile and the shared parameter is required.\n"); abort = true; }
}else { current->setSharedFile(sharedfile); }
//////////////////////////////////////////////////////////////////////
////////// example of getting other types of parameters //////////////
//////////////////////////////////////////////////////////////////////
//use only one Mutliple type
method = validParameter.valid(parameters, "method");
if (method == "not found") { method = "average"; }
if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { }
else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average, and weighted.\n"); abort = true; }
//use more than one multiple type. do not check to make sure the entry is valid.
string calc = validParameter.valid(parameters, "calc");
if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
else {
if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
}
util.splitAtDash(calc, Estimators);
//Boolean type - m->isTrue looks for t, true, f or false and is case insensitive
string timing = validParameter.valid(parameters, "timing");
if (timing == "not found") { timing = "F"; }
useTiming = util.isTrue(timing);
//Number type - mothurConvert makes sure the convert can happen to avoid a crash.
string temp = validParameter.valid(parameters, "processors"); if (temp == "not found"){ temp = current->getProcessors(); }
processors = current->setProcessors(temp);
//Groups must be checked later to make sure they are valid. SharedUtilities has functions of check the validity, just make to so m->setGroups() after the checks. If you are using these with a shared file no need to check the SharedRAbundVector class will call SharedUtilites for you, kinda nice, huh?
string groups = validParameter.valid(parameters, "groups");
if (groups == "not found") { groups = ""; }
else {
util.splitAtDash(groups, Groups);
if (Groups.size() != 0) { if (Groups[0]== "all") { Groups.clear(); } }
}
//Commonly used to process list, rabund, sabund, shared and relabund files. Look at "smart distancing" examples below in the execute function.
string label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = false; }
else { allLines = true; }
}
//if your command has a namefile as an option, you may want ot check to see if there is a current namefile
//saved by mothur that is associated with the other files you are using as inputs.
//You can do so by adding the files associated with the namefile to the files vector and then asking parser to check.
}
}
catch(exception& e) {
m->errorOut(e, "NewCommand", "NewCommand");
exit(1);
}
}
//**********************************************************************************************************************
int NewCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
/*
InputData input(inputFileName, format, Groups);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
if (format == "relabund") {
SharedRAbundFloatVectors* lookup = util.getNextRelabund(input, allLines, userLabels, processedLabels, lastLabel);
Groups = lookup->getNamesGroups();
while (lookup != nullptr) {
if (m->getControl_pressed()) { delete lookup; break; }
//////// myfunction(lookup); - call your function to process relabund data ////////////////////
delete lookup;
lookup = util.getNextRelabund(input, allLines, userLabels, processedLabels, lastLabel);
}
}else if (format == "sharedfile") {
SharedRAbundVectors* lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
Groups = lookup->getNamesGroups();
while (lookup != nullptr) {
if (m->getControl_pressed()) { delete lookup; break; }
//////// myfunction(lookup); - call your function to process shared data ////////////////////
delete lookup;
lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
}
}else if (format == "list") {
ListVector* list = util.getNextList(input, allLines, userLabels, processedLabels, lastLabel);
while (list != nullptr) {
if (m->getControl_pressed()) { delete list; break; }
//////// myfunction(list); - call your function to process list data //////////////////// delete list;
list = util.getNextList(input, allLines, userLabels, processedLabels, lastLabel);
}
}else if (format == "rabund") {
RAbundVector* rabund = util.getNextRAbund(input, allLines, userLabels, processedLabels, lastLabel);
while (rabund != nullptr) {
if (m->getControl_pressed()) { delete rabund; break; }
//////// myfunction(rabund); - call your function to process list data //////////////////// delete rabund;
rabund = util.getNextRAbund(input, allLines, userLabels, processedLabels, lastLabel);
}
}
*/
//if you make a new file or a type that mothur keeps track of the current version, you can update it with something like the following.
string currentFasta = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; current->setFastaFile(currentFasta); }
}
//output files created by command
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "NewCommand", "NewCommand");
exit(1);
}
}
//**********************************************************************************************************************
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