--- /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 {
+ 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(); remove((output+".temp").c_str()); }
+
+ Command* thisCommand = commandFactory->getCommand(it->first);
+
+ //don't add hidden commands
+ if (thisCommand->getCommandCategory() != "Hidden") {
+ numNonHidden++;
+
+ //general info
+ out << "commandName=" << thisCommand->getCommandName() << 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;
+
+ //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);
+ remove((output+".temp").c_str());
+
+ 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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