command.hpp

   1 #ifndef COMMAND_HPP
   2 #define COMMAND_HPP
   3 //test2
   4 /*
   5  *  command.h
   6  *  nast
   7  *
   8  *  Created by Pat Schloss on 10/23/08.
   9  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
  10  *
  11  */
  12
  13 /*This class is a parent to all the command classes.  */
  14
  15
  16 #include "mothur.h"
  17 #include "optionparser.h"
  18 #include "validparameter.h"
  19 #include "mothurout.h"
  20 #include "commandparameter.h"
  21
  22
  23 class Command {
  24
  25         public:
  26                 Command() {  m = MothurOut::getInstance();   }
  27
  28                 //needed by gui
  29                 virtual string getCommandName() = 0;
  30                 virtual string getCommandCategory() = 0;
  31                 virtual string getHelpString() = 0;
  32                 virtual string getCitation() = 0;
  33                 virtual string getDescription() = 0;
  34
  35                 virtual map<string, vector<string> > getOutputFiles() { return outputTypes; }
  36         string getOutputFileName(string type, map<string, string> variableParts) {  //uses the pattern to create an output filename for a given type and input file name.
  37                try {
  38                     string filename = "";
  39                     map<string, vector<string> >::iterator it;
  40
  41                     //is this a type this command creates
  42                     it = outputTypes.find(type);
  43                     if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  44                     else {
  45
  46                         string patternTemp = getOutputPattern(type);
  47                         vector<string> patterns;
  48                         m->splitAtDash(patternTemp, patterns);
  49
  50                         //find pattern to use based on number of variables passed in
  51                         string pattern = "";
  52                         bool foundPattern = false;
  53                         vector<int> numVariablesPerPattern;
  54                         for (int i = 0; i < patterns.size(); i++) {
  55                             int numVariables = 0;
  56                             for (int j = 0; j < patterns[i].length(); j++) { if (patterns[i][j] == '[') { numVariables++; } }
  57                             numVariablesPerPattern.push_back(numVariables);
  58
  59                             if (numVariables == variableParts.size()) { pattern = patterns[i]; foundPattern = true; break; }
  60                         }
  61
  62                         //if you didn't find an exact match do we have something that might work
  63                         if (!foundPattern) {
  64                             for (int i = 0; i < numVariablesPerPattern.size(); i++) {
  65                                 if (numVariablesPerPattern[i] < variableParts.size()) { pattern = patterns[i]; foundPattern = true; break; }
  66                             }
  67                             if (!foundPattern) {  m->mothurOut("[ERROR]: Not enough variable pieces for " + type + ".\n"); m->control_pressed = true; }
  68                         }
  69
  70                         if (pattern != "") {
  71                             int numVariables = 0;
  72                             for (int i = 0; i < pattern.length(); i++) { if (pattern[i] == '[') { numVariables++; } }
  73
  74                             vector<string> pieces;
  75                             m->splitAtComma(pattern, pieces);
  76
  77
  78                             for (int i = 0; i < pieces.size(); i++) {
  79                                 if (pieces[i][0] == '[') {
  80                                     map<string, string>::iterator it = variableParts.find(pieces[i]);
  81                                     if (it == variableParts.end()) {
  82                                         m->mothurOut("[ERROR]: Did not provide variable for " + pieces[i] + ".\n"); m->control_pressed = true;
  83                                     }else {
  84                                         if (it->second != "") {
  85                                             if (it->first == "[filename]") { filename += it->second; }
  86                                             else if (it->first == "[extension]") {
  87                                                 if (filename.length() > 0) { //rip off last "."
  88                                                     filename = filename.substr(0, filename.length()-1);
  89                                                 }
  90                                                 filename += it->second + ".";
  91                                             }else { filename += it->second + "."; }
  92                                         }
  93                                     }
  94                                 }else {
  95                                     filename += pieces[i] + ".";
  96                                 }
  97                             }
  98                             if (filename.length() > 0) { //rip off last "."
  99                                 filename = filename.substr(0, filename.length()-1);
 100                             }
 101                         }
 102                     }
 103                     return filename;
 104                 }
 105                 catch(exception& e) {
 106                     m->errorOut(e, "command", "getOutputFileName");
 107                     exit(1);
 108                 }
 109         }
 110
 111         virtual string getOutputPattern(string) = 0; //pass in type, returns something like: [filename],align or [filename],[distance],subsample.shared  strings in [] means its a variable.  This is used by the gui to predict output file names.  use variable keywords: [filename], [distance], [group], [extension], [tag]
 112                 virtual vector<string> setParameters() = 0; //to fill parameters
 113                 virtual vector<CommandParameter> getParameters() { return parameters; }
 114
 115                 virtual int execute() = 0;
 116                 virtual void help() = 0;
 117                 void citation() { m->mothurOutEndLine(); m->mothurOut(getCitation()); m->mothurOutEndLine(); }
 118                 virtual ~Command() { }
 119
 120         protected:
 121                 MothurOut* m;
 122                 bool calledHelp;
 123
 124                 map<string, vector<string> > outputTypes;
 125                 vector<CommandParameter> parameters;
 126
 127                 map<string, vector<string> >::iterator itTypes;
 128 };
 129
 130 #endif