changes while testing

[mothur.git] / getcommandinfocommand.cpp

diff --git a/getcommandinfocommand.cpp b/getcommandinfocommand.cpp
index 7ca245369136a19da6ec607d0055a1b0351d2cc7..b61236dbac71421d0e63a2dbd5c89071182652e2 100644 (file)
--- a/getcommandinfocommand.cpp
+++ b/getcommandinfocommand.cpp
@@ -12,9 +12,9 @@
 //**********************************************************************************************************************
 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);
+               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);          }
@@ -45,6 +45,7 @@ GetCommandInfoCommand::GetCommandInfoCommand(string option)  {
                
                //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();
@@ -91,7 +92,7 @@ int GetCommandInfoCommand::execute(){
                //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()); }
+                       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);
                        
@@ -101,6 +102,7 @@ int GetCommandInfoCommand::execute(){
                                
                                //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
@@ -111,17 +113,31 @@ int GetCommandInfoCommand::execute(){
                                }
                                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; }
+                               if (thisOutputTypes.size() == 0) { out << "outputTypesNames=0" << endl; }
                                else {
-                                       string types = "";
-                                       for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) {  types += itTypes->first + "-";  }
+                                       //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;
+                                       //types = types.substr(0, types.length()-1);
+                                       out << "outputTypesNames=" << thisOutputTypes.size() << endl;
+                    
+                    for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) {
+                        out << itTypes->first << "=" << thisCommand->getOutputPattern(itTypes->first) << endl;
+                    }
                                }
                                
                                vector<string> booleans; vector<string> numbers; vector<string> multiples; vector<string> Strings;
@@ -174,7 +190,7 @@ int GetCommandInfoCommand::execute(){
                out2.close();
                
                m->appendFiles(output+".temp", output);
-               remove((output+".temp").c_str());
+               m->mothurRemove((output+".temp"));
        
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -200,34 +216,54 @@ int GetCommandInfoCommand::getInfo(vector<CommandParameter> para, vector<string>
                for (int i = 0; i < para.size(); i++) {
                        if ((para[i].name == "inputdir") || (para[i].name == "outputdir")) {} //ignore
                        else {
+                string important = "|F";
+                if (para[i].important || para[i].required) { important = "|T"; }
+                
+                string outputType = "|none";
+                if (para[i].outputTypes != "") { outputType = "|" + para[i].outputTypes; }
+                
                                if (para[i].type == "Boolean") {
-                                       string temp = para[i].name + "=" + para[i].optionsDefault;
+                                       string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
                                        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;
+                                       string temp = para[i].name + "=" + para[i].options + "|" + para[i].optionsDefault + "|" + multAllowed + important + outputType;
                                        multiples.push_back(temp);
                                }else if (para[i].type == "Number") {
-                                       string temp = para[i].name + "=" + para[i].optionsDefault;
+                                       string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
                                        numbers.push_back(temp);
                                }else if (para[i].type == "String") {
-                                       string temp = para[i].name + "=" + para[i].optionsDefault;
+                                       string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
                                        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;
+                                       string temp = required + important + "|" + para[i].chooseOnlyOneGroup + "|" + para[i].chooseAtLeastOneGroup + "|" + para[i].linkedGroup + outputType;
                                        inputTypes[para[i].name] = temp;
                                        
                                        //add choose only one groups
-                                       groups[para[i].chooseOnlyOneGroup].insert(para[i].name);
-                                       
+                    vector<string> tempGroups;
+                    m->splitAtDash(para[i].chooseOnlyOneGroup, tempGroups);
+                    for (int l = 0; l < tempGroups.size(); l++) {
+                        groups[tempGroups[l]].insert(para[i].name);
+                    }
+                                       tempGroups.clear();
+                    
                                        //add at least one group names
-                                       groups[para[i].chooseAtLeastOneGroup].insert(para[i].name);
+                    m->splitAtDash(para[i].chooseAtLeastOneGroup, tempGroups);
+                    for (int l = 0; l < tempGroups.size(); l++) {
+                        groups[tempGroups[l]].insert(para[i].name);
+                    }
+                                       tempGroups.clear();
+                                       
                                        
                                        //add at linked group names
-                                       groups[para[i].linkedGroup].insert(para[i].name);
+                    m->splitAtDash(para[i].linkedGroup, tempGroups);
+                    for (int l = 0; l < tempGroups.size(); l++) {
+                        groups[tempGroups[l]].insert(para[i].name);
+                    }
+                                       tempGroups.clear();
                                                  
                                }else { m->mothurOut("[ERROR]: " + para[i].type + " is an unknown parameter type, please correct."); m->mothurOutEndLine(); }
                        }