+++ /dev/null
-/*
- * getcommandinfo.cpp
- * Mothur
- *
- * Created by westcott on 4/6/11.
- * Copyright 2011 Schloss Lab. All rights reserved.
- *
- */
-
-#include "getcommandinfocommand.h"
-
-//**********************************************************************************************************************
-vector<string> GetCommandInfoCommand::setParameters(){
- try {
- CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
- 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, "GetCommandInfoCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string GetCommandInfoCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "This command is used by the gui to get the information about current commands available in mothur.\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "GetCommandInfoCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-GetCommandInfoCommand::GetCommandInfoCommand(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 {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string, string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
- //check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- output = validParameter.validFile(parameters, "output", false);
- if (output == "not found") { output = ""; m->mothurOut("You must provide an output filename."); m->mothurOutEndLine(); abort=true; }
-
- }
- }
- catch(exception& e) {
- m->errorOut(e, "GetCommandInfoCommand", "GetCommandInfoCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int GetCommandInfoCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- commandFactory = CommandFactory::getInstance();
-
- ofstream out;
- m->openOutputFile(output+".temp", out);
-
- int numNonHidden = 0;
-
- out << "mothurLocation=" << m->getFullPathName(m->argv) << endl;
- out << "mothurVersion=" << m->getVersion() << endl;
-
- map<string, string> commands = commandFactory->getListCommands();
- map<string, string>::iterator it;
-
- //loop through each command outputting info
- for (it = commands.begin(); it != commands.end(); it++) {
-
- if (m->control_pressed) { m->mothurOut("[ERROR]: did not complete making the file."); m->mothurOutEndLine(); out.close(); m->mothurRemove((output+".temp")); }
-
- Command* thisCommand = commandFactory->getCommand(it->first);
-
- //don't add hidden commands
- if (thisCommand->getCommandCategory() != "Hidden") {
- numNonHidden++;
-
- //general info
- out << "commandName=" << thisCommand->getCommandName() << endl;
- //cout << thisCommand->getCommandName() << " current citation = " << thisCommand->getCitation() << endl;
- out << "commandCategory=" << thisCommand->getCommandCategory() << endl;
-
- //remove /n from help string since gui reads line by line
- string myhelpString = thisCommand->getHelpString();
- string newHelpString = "";
- for (int i = 0; i < myhelpString.length(); i++) {
- if (myhelpString[i] != '\n') { newHelpString += myhelpString[i]; }
- }
- out << "help=" << newHelpString << endl;
-
- //remove /n from citation string since gui reads line by line
- string mycitationString = thisCommand->getCitation();
- string newCitationString = "";
- for (int i = 0; i < mycitationString.length(); i++) {
- if (mycitationString[i] != '\n') { newCitationString += mycitationString[i]; }
- }
- out << "citation=" << newCitationString << endl;
-
- out << "description=" << thisCommand->getDescription() << endl;
-
- //outputTypes - makes something like outputTypes=fasta-name-qfile
- map<string, vector<string> > thisOutputTypes = thisCommand->getOutputFiles();
- map<string, vector<string> >::iterator itTypes;
-
- if (thisOutputTypes.size() == 0) { out << "outputTypes=none" << endl; }
- else {
- string types = "";
- for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) { types += itTypes->first + "-"; }
- //rip off last -
- types = types.substr(0, types.length()-1);
- out << "outputTypes=" << types << endl;
- }
-
- vector<string> booleans; vector<string> numbers; vector<string> multiples; vector<string> Strings;
- vector<string> inputGroupNames; map<string, string> inputTypes;
-
- getInfo(thisCommand->getParameters(), booleans, numbers, multiples, Strings, inputGroupNames, inputTypes);
-
- //output booleans
- out << "Boolean=" << booleans.size() << endl;
- for (int i = 0; i < booleans.size(); i++) { out << booleans[i] << endl; }
-
- //output mulitples
- out << "Multiple=" << multiples.size() << endl;
- for (int i = 0; i < multiples.size(); i++) { out << multiples[i] << endl; }
-
- //output numbers
- out << "Numbers=" << numbers.size() << endl;
- for (int i = 0; i < numbers.size(); i++) { out << numbers[i] << endl; }
-
- //output strings
- out << "String=" << Strings.size() << endl;
- for (int i = 0; i < Strings.size(); i++) { out << Strings[i] << endl; }
-
- //output groups
- out << "inputGroupNames=" << inputGroupNames.size() << endl;
- for (int i = 0; i < inputGroupNames.size(); i++) { out << inputGroupNames[i] << endl; }
-
- //output input types
- if (inputTypes.size() == 0) { out << "inputTypes=" << endl; }
- else {
- string types = "";
- for (map<string, string>::iterator it2 = inputTypes.begin(); it2 != inputTypes.end(); it2++) { types += it2->first + "-"; }
- //rip off last -
- types = types.substr(0, types.length()-1);
- out << "inputTypes=" << types << endl;
-
- for (map<string, string>::iterator it2 = inputTypes.begin(); it2 != inputTypes.end(); it2++) {
- out << it2->first << "=" << it2->second << endl;
- }
- }
-
- }
- }
-
- out.close();
-
- ofstream out2;
- m->openOutputFile(output, out2);
- out2 << numNonHidden << endl;
- out2.close();
-
- m->appendFiles(output+".temp", output);
- m->mothurRemove((output+".temp"));
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(output); m->mothurOutEndLine();
- m->mothurOutEndLine();
-
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "GetCommandInfoCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int GetCommandInfoCommand::getInfo(vector<CommandParameter> para, vector<string>& booleans, vector<string>& numbers, vector<string>& multiples, vector<string>& strings, vector<string>& inputGroupNames, map<string, string>& inputTypes){
- try {
-
- map<string, set<string> > groups;
- map<string, set<string> >::iterator itGroups;
-
- for (int i = 0; i < para.size(); i++) {
- if ((para[i].name == "inputdir") || (para[i].name == "outputdir")) {} //ignore
- else {
- if (para[i].type == "Boolean") {
- string temp = para[i].name + "=" + para[i].optionsDefault;
- booleans.push_back(temp);
- }else if (para[i].type == "Multiple") {
- string multAllowed = "F";
- if (para[i].multipleSelectionAllowed) { multAllowed = "T"; }
- string temp = para[i].name + "=" + para[i].options + "|" + para[i].optionsDefault + "|" + multAllowed;
- multiples.push_back(temp);
- }else if (para[i].type == "Number") {
- string temp = para[i].name + "=" + para[i].optionsDefault;
- numbers.push_back(temp);
- }else if (para[i].type == "String") {
- string temp = para[i].name + "=" + para[i].optionsDefault;
- strings.push_back(temp);
- }else if (para[i].type == "InputTypes") {
- string required = "F";
- if (para[i].required) { required = "T"; }
- string temp = required + "|" + para[i].chooseOnlyOneGroup + "|" + para[i].chooseAtLeastOneGroup + "|" + para[i].linkedGroup;
- inputTypes[para[i].name] = temp;
-
- //add choose only one groups
- groups[para[i].chooseOnlyOneGroup].insert(para[i].name);
-
- //add at least one group names
- groups[para[i].chooseAtLeastOneGroup].insert(para[i].name);
-
- //add at linked group names
- groups[para[i].linkedGroup].insert(para[i].name);
-
- }else { m->mothurOut("[ERROR]: " + para[i].type + " is an unknown parameter type, please correct."); m->mothurOutEndLine(); }
- }
- }
-
- for (itGroups = groups.begin(); itGroups != groups.end(); itGroups++) {
- if (itGroups->first != "none") {
- set<string> tempNames = itGroups->second;
- string temp = itGroups->first + "=";
- for (set<string>::iterator itNames = tempNames.begin(); itNames != tempNames.end(); itNames++) {
- temp += *itNames + "-";
- }
- //rip off last -
- temp = temp.substr(0, temp.length()-1);
- inputGroupNames.push_back(temp);
- }
- }
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetCommandInfoCommand", "getInfo");
- exit(1);
- }
-}
-//**********************************************************************************************************************/
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