filterseqscommand.cpp

   1 /*
   2  *  filterseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 5/4/09.
   6  *  Copyright 2009 __MyCompanyName__. All rights reserved.
   7  *
   8  */
   9
  10 #include "filterseqscommand.h"
  11 #include <iostream>
  12 #include <fstream>
  13
  14 /**************************************************************************************/
  15 void FilterSeqsCommand::doTrump() {
  16         //trump = globaldata->getTrump();
  17 //
  18 //      for(int i = 0; i < db->size(); i++) {
  19 //              Sequence cur = db->get(i);
  20 //              string curAligned = cur.getAligned();
  21 //
  22 //              for(int j = 0; j < curAligned.length-1; j++) {
  23 //                      string curChar = curAligned.substr(j, j+1);
  24 //
  25 //                      if(curChar.compare(trump) == 0)
  26 //                              columnsToRemove[j] = true;
  27 //              }
  28 //      }
  29 }
  30
  31 /**************************************************************************************/
  32 void FilterSeqsCommand::doSoft() {
  33         //soft = atoi(globaldata->getSoft().c_str());
  34 //      vector<vector<int> > columnSymbolSums;
  35 //      vector<vector<string> > columnSymbols;
  36 //      for(int i = 0; i < db->get(0).getLength(); i++) {
  37 //              vector<string> symbols;
  38 //              vector<int> sums;
  39 //              columnSymbols[i] = symbols;
  40 //              columnSymbolSums[i] = sums;
  41 //      }
  42 //
  43 //      for(int i = 0; i < db->size(); i++) {
  44 //              Sequence cur = db->get(i);
  45 //              string curAligned = cur.getAligned();
  46 //
  47 //              for(int j = 0; j < curAligned.length-1; j++) {
  48 //                      string curChar = curAligned.substr(j, j+1);
  49 //                      vector<string> curColumnSymbols = columnSymbols[j];
  50 //
  51 //                      bool newSymbol = true;
  52 //
  53 //                      for(int k = 0; j < curColumnSymbols.size(); j++)
  54 //                              if(curChar.compare(curColumnSymbols[k]) == 0) {
  55 //                                      newSymbol = false;
  56 //                                      columnSymbolSums[j][k]++;
  57 //                              }
  58 //
  59 //                      if(newSymbol) {
  60 //                              columnSymbols.push_back(curChar);
  61 //                              columnSymbolSums[j].push_back(1);
  62 //                      }
  63 //              }
  64 //      }
  65 //
  66 //      for(int i = 0; i < columnSymbolSums.size(); i++) {
  67 //              int totalSum = 0;
  68 //              int max = 0;
  69 //              vector<int> curColumn = columnSymbolSums[i];
  70 //
  71 //              for(int j = 0; j < curColumn.size(); j++) {
  72 //                      int curSum = curColumn[j];
  73 //                      if(curSum > max)
  74 //                              max = curSum;
  75 //                      totalSum += curSum;
  76 //              }
  77 //
  78 //              if((double)max/(double)totalSum * 100 < soft)
  79 //                      columnsToRemove[i] = true;
  80 //      }
  81 }
  82 void FilterSeqsCommand::doFilter() {}
  83 /**************************************************************************************/
  84 int FilterSeqsCommand::execute() {
  85         try {
  86                 globaldata = GlobalData::getInstance();
  87                 filename = globaldata->inputFileName;
  88
  89                 if(globaldata->getFastaFile().compare("") != 0) {
  90                         readFasta = new ReadFasta(filename);
  91                         readFasta->read();
  92                         db = readFasta->getDB();
  93                 }
  94
  95                 else if(globaldata->getNexusFile().compare("") != 0) {
  96                         readNexus = new ReadNexus(filename);
  97                         readNexus->read();
  98                         db = readNexus->getDB();
  99                 }
 100
 101                 else if(globaldata->getClustalFile().compare("") != 0) {
 102                         readClustal = new ReadClustal(filename);
 103                         readClustal->read();
 104                         db = readClustal->getDB();
 105                 }
 106
 107                 else if(globaldata->getPhylipFile().compare("") != 0) {
 108                         readPhylip = new ReadPhylip(filename);
 109                         readPhylip->read();
 110                         db = readPhylip->getDB();
 111                 }
 112
 113                 for(int i = 0; i < db->get(0).getLength(); i++)
 114                         columnsToRemove[i] = false;
 115
 116                 // Trump
 117                 if(globaldata->getTrump().compare("") != 0) {
 118
 119
 120                 }
 121
 122                 // Soft
 123                 if(globaldata->getSoft().compare("") != 0) {}
 124
 125
 126
 127
 128                 // Filter
 129                 //if(globaldata->getFilter().compare("") != 0) {
 130 //
 131 //                      filter = globaldata->getFilter();
 132 //                      ifstream filehandle;
 133 //                      openInputFile(filter, filehandle);
 134 //
 135 //                      char c;
 136 //                      int count = 0;
 137 //                      while(!filehandle.eof()) {
 138 //                              c = filehandle.get();
 139 //                              if(c == '0')
 140 //                                      columnsToRemove[count] = true;
 141 //                              count++;
 142 //                      }
 143 //              }
 144
 145
 146
 147
 148
 149                 return 0;
 150         }
 151         catch(exception& e) {
 152                 cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 153                 exit(1);
 154         }
 155         catch(...) {
 156                 cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 157                 exit(1);
 158         }
 159 }
 160 /**************************************************************************************/