X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcommandinfocommand.cpp;fp=getcommandinfocommand.cpp;h=7ca245369136a19da6ec607d0055a1b0351d2cc7;hb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;hp=0000000000000000000000000000000000000000;hpb=c7f5a50aec1ec4b420b286d6ccf980d2a847d494;p=mothur.git

diff --git a/getcommandinfocommand.cpp b/getcommandinfocommand.cpp
new file mode 100644
index 0000000..7ca2453
--- /dev/null
+++ b/getcommandinfocommand.cpp
@@ -0,0 +1,257 @@
+/*
+ *  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);
+	}
+}
+//**********************************************************************************************************************/