sequencedb.cpp

   1 /*
   2  *  sequencedb.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 4/13/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "sequencedb.h"
  11 #include "sequence.hpp"
  12 #include "mothur.h"
  13 #include "calculator.h"
  14
  15
  16 /***********************************************************************/
  17
  18 SequenceDB::SequenceDB() {}
  19 /***********************************************************************/
  20 //the clear function free's the memory
  21 SequenceDB::~SequenceDB() { clear(); }
  22
  23 /***********************************************************************/
  24
  25 SequenceDB::SequenceDB(int newSize) {
  26         data.resize(newSize, Sequence());
  27 }
  28
  29 /***********************************************************************/
  30
  31 SequenceDB::SequenceDB(ifstream& filehandle) {
  32         try{
  33
  34                 //read through file
  35                 while (!filehandle.eof()) {
  36                         //input sequence info into sequencedb
  37                         Sequence newSequence(filehandle);
  38                         data.push_back(newSequence);
  39
  40                         //takes care of white space
  41                         gobble(filehandle);
  42                 }
  43
  44                 filehandle.close();
  45
  46         }
  47         catch(exception& e) {
  48                 errorOut(e, "SequenceDB", "SequenceDB");
  49                 exit(1);
  50         }
  51 }
  52 /*******************************************************************************/
  53 string SequenceDB::readName(ifstream& in) {
  54         try{
  55                 string name = "";
  56                 int c;
  57                 string temp;
  58
  59                 while ((c = in.get()) != EOF) {
  60                         //if c is not a line return
  61                         if (c != 10) {
  62                                 name += c;
  63                         }else { break;  }
  64                 }
  65
  66                 return name;
  67         }
  68         catch(exception& e) {
  69                 errorOut(e, "SequenceDB", "readName");
  70                 exit(1);
  71         }
  72 }
  73
  74 /*******************************************************************************/
  75 string SequenceDB::readSequence(ifstream& in) {
  76         try{
  77                 string sequence = "";
  78                 string line;
  79                 int pos, c;
  80
  81                 while (!in.eof()) {
  82                         //save position in file in case next line is a new name.
  83                         pos = in.tellg();
  84                         line = "";
  85                         in >> line;
  86                         //if you are at a new name
  87                         if (line[0] == '>') {
  88                                 //put file pointer back since you are now at a new name
  89                                 in.seekg(pos, ios::beg);
  90                                 c = in.get();  //because you put it back to a newline char
  91                                 break;
  92                         }else {  sequence += line;      }
  93                 }
  94
  95                 return sequence;
  96         }
  97         catch(exception& e) {
  98                 errorOut(e, "SequenceDB", "readSequence");
  99                 exit(1);
 100         }
 101 }
 102
 103 /***********************************************************************/
 104
 105 int SequenceDB::getNumSeqs() {
 106         return data.size();
 107 }
 108
 109 /***********************************************************************/
 110
 111 void SequenceDB::set(int index, string newUnaligned) {
 112         try {
 113                 data[index] = Sequence(data[index].getName(), newUnaligned);
 114         }
 115         catch(exception& e) {
 116                 errorOut(e, "SequenceDB", "set");
 117                 exit(1);
 118         }
 119 }
 120
 121 /***********************************************************************/
 122
 123 void SequenceDB::set(int index, Sequence newSeq) {
 124         try {
 125                 data[index] = newSeq;
 126         }
 127         catch(exception& e) {
 128                 errorOut(e, "SequenceDB", "set");
 129                 exit(1);
 130         }
 131 }
 132
 133 /***********************************************************************/
 134
 135 Sequence SequenceDB::get(int index) {
 136         return data[index];
 137 }
 138
 139 /***********************************************************************/
 140
 141 void SequenceDB::resize(int newSize) {
 142         try {
 143                 data.resize(newSize);
 144         }
 145         catch(exception& e) {
 146                 errorOut(e, "SequenceDB", "resize");
 147                 exit(1);
 148         }
 149 }
 150
 151 /***********************************************************************/
 152
 153 void SequenceDB::clear() {
 154         try {
 155                 data.clear();
 156         }
 157         catch(exception& e) {
 158                 errorOut(e, "SequenceDB", "clear");
 159                 exit(1);
 160         }
 161 }
 162
 163 /***********************************************************************/
 164
 165 int SequenceDB::size() {
 166         return data.size();
 167 }
 168
 169 /***********************************************************************/
 170
 171 void SequenceDB::print(ostream& out) {
 172         try {
 173                 for(int i = 0; i < data.size(); i++) {
 174                         data[i].printSequence(out);
 175                 }
 176         }
 177         catch(exception& e) {
 178                 errorOut(e, "SequenceDB", "print");
 179                 exit(1);
 180         }
 181 }
 182
 183 /***********************************************************************/
 184
 185 void SequenceDB::push_back(Sequence newSequence) {
 186         try {
 187                 data.push_back(newSequence);
 188         }
 189         catch(exception& e) {
 190                 errorOut(e, "SequenceDB", "push_back");
 191                 exit(1);
 192         }
 193 }
 194
 195 /***********************************************************************/
 196