secondarystructurecommand.cpp

   1 /*
   2  *  secondarystructurecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/18/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "secondarystructurecommand.h"
  11 #include "sequence.hpp"
  12
  13 //**********************************************************************************************************************
  14
  15 AlignCheckCommand::AlignCheckCommand(string option){
  16         try {
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"fasta","map"};
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string,string> parameters = parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31
  32                         //check to make sure all parameters are valid for command
  33                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  34                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  35                         }
  36
  37                         //check for required parameters
  38                         mapfile = validParameter.validFile(parameters, "map", true);
  39                         if (mapfile == "not open") { abort = true; }
  40                         else if (mapfile == "not found") {  mapfile = "";  mothurOut("You must provide an map file."); mothurOutEndLine(); abort = true; }
  41
  42                         fastafile = validParameter.validFile(parameters, "fasta", true);
  43                         if (fastafile == "not open") { abort = true; }
  44                         else if (fastafile == "not found") {  fastafile = "";  mothurOut("You must provide an fasta file."); mothurOutEndLine(); abort = true;  }
  45
  46                 }
  47
  48         }
  49         catch(exception& e) {
  50                 errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand");
  51                 exit(1);
  52         }
  53 }
  54 //**********************************************************************************************************************
  55
  56 void AlignCheckCommand::help(){
  57         try {
  58                 //mothurOut("The remove.seqs command reads an .accnos file and one of the following file types: fasta, name, group or alignreport file.\n");
  59                 //mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
  60                 //mothurOut("The remove.seqs command parameters are accnos, fasta, name, group and alignreport.  You must provide accnos and one of the other parameters.\n");
  61                 //mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
  62                 //mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
  63                 //mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
  64         }
  65         catch(exception& e) {
  66                 errorOut(e, "AlignCheckCommand", "help");
  67                 exit(1);
  68         }
  69 }
  70
  71 //**********************************************************************************************************************
  72
  73 int AlignCheckCommand::execute(){
  74         try {
  75
  76                 if (abort == true) { return 0; }
  77
  78                 //get secondary structure info.
  79                 readMap();
  80
  81
  82
  83                 return 0;
  84         }
  85
  86         catch(exception& e) {
  87                 errorOut(e, "AlignCheckCommand", "execute");
  88                 exit(1);
  89         }
  90 }
  91 //**********************************************************************************************************************
  92 void AlignCheckCommand::readMap(){
  93         try {
  94
  95                 structMap.resize(1, 0);
  96                 ifstream in;
  97
  98                 openInputFile(mapfile, in);
  99
 100                 while(!in.eof()){
 101                         int position;
 102                         in >> position;
 103                         structMap.push_back(position);
 104                         gobble(in);
 105                 }
 106                 in.close();
 107
 108                 seqLength = structMap.size();
 109
 110
 111                 //check you make sure is structMap[10] = 380 then structMap[380] = 10.
 112                 for(int i=0;i<seqLength;i++){
 113                         if(structMap[i] != 0){
 114                                 if(structMap[structMap[i]] != i){
 115                                         mothurOut("Your map file contains an error:  line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); mothurOutEndLine();
 116                                 }
 117                         }
 118                 }
 119
 120
 121         }
 122         catch(exception& e) {
 123                 errorOut(e, "AlignCheckCommand", "readFasta");
 124                 exit(1);
 125         }
 126 }
 127
 128 //**********************************************************************************************************************