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                 string name, sequence, line;
  34                 sequence = "";
  35                 int c;
  36                 string temp;
  37
  38
  39                 //read through file
  40                 while ((c = filehandle.get()) != EOF) {
  41                         name = ""; sequence = "";
  42                         //is this a name
  43                         if (c == '>') {
  44                                 name = readName(filehandle);
  45                                 sequence = readSequence(filehandle);
  46                         }else {  mothurOut("Error fasta in your file. Please correct."); mothurOutEndLine(); }
  47
  48                         //input sequence info into sequencedb
  49                         Sequence newSequence(name, sequence);
  50                         data.push_back(newSequence);
  51
  52                         //takes care of white space
  53                         gobble(filehandle);
  54                 }
  55
  56                 filehandle.close();
  57
  58         }
  59         catch(exception& e) {
  60                 errorOut(e, "SequenceDB", "SequenceDB");
  61                 exit(1);
  62         }
  63 }
  64 /*******************************************************************************/
  65 string SequenceDB::readName(ifstream& in) {
  66         try{
  67                 string name = "";
  68                 int c;
  69                 string temp;
  70
  71                 while ((c = in.get()) != EOF) {
  72                         //if c is not a line return
  73                         if (c != 10) {
  74                                 name += c;
  75                         }else { break;  }
  76                 }
  77
  78                 return name;
  79         }
  80         catch(exception& e) {
  81                 errorOut(e, "SequenceDB", "readName");
  82                 exit(1);
  83         }
  84 }
  85
  86 /*******************************************************************************/
  87 string SequenceDB::readSequence(ifstream& in) {
  88         try{
  89                 string sequence = "";
  90                 string line;
  91                 int pos, c;
  92
  93                 while (!in.eof()) {
  94                         //save position in file in case next line is a new name.
  95                         pos = in.tellg();
  96                         line = "";
  97                         in >> line;
  98                         //if you are at a new name
  99                         if (line[0] == '>') {
 100                                 //put file pointer back since you are now at a new name
 101                                 in.seekg(pos, ios::beg);
 102                                 c = in.get();  //because you put it back to a newline char
 103                                 break;
 104                         }else {  sequence += line;      }
 105                 }
 106
 107                 return sequence;
 108         }
 109         catch(exception& e) {
 110                 errorOut(e, "SequenceDB", "readSequence");
 111                 exit(1);
 112         }
 113 }
 114
 115 /***********************************************************************/
 116
 117 int SequenceDB::getNumSeqs() {
 118         return data.size();
 119 }
 120
 121 /***********************************************************************/
 122
 123 void SequenceDB::set(int index, string newUnaligned) {
 124         try {
 125                 data[index] = Sequence(data[index].getName(), newUnaligned);
 126         }
 127         catch(exception& e) {
 128                 errorOut(e, "SequenceDB", "set");
 129                 exit(1);
 130         }
 131 }
 132
 133 /***********************************************************************/
 134
 135 void SequenceDB::set(int index, Sequence newSeq) {
 136         try {
 137                 data[index] = newSeq;
 138         }
 139         catch(exception& e) {
 140                 errorOut(e, "SequenceDB", "set");
 141                 exit(1);
 142         }
 143 }
 144
 145 /***********************************************************************/
 146
 147 Sequence SequenceDB::get(int index) {
 148         return data[index];
 149 }
 150
 151 /***********************************************************************/
 152
 153 void SequenceDB::resize(int newSize) {
 154         try {
 155                 data.resize(newSize);
 156         }
 157         catch(exception& e) {
 158                 errorOut(e, "SequenceDB", "resize");
 159                 exit(1);
 160         }
 161 }
 162
 163 /***********************************************************************/
 164
 165 void SequenceDB::clear() {
 166         try {
 167                 data.clear();
 168         }
 169         catch(exception& e) {
 170                 errorOut(e, "SequenceDB", "clear");
 171                 exit(1);
 172         }
 173 }
 174
 175 /***********************************************************************/
 176
 177 int SequenceDB::size() {
 178         return data.size();
 179 }
 180
 181 /***********************************************************************/
 182
 183 void SequenceDB::print(ostream& out) {
 184         try {
 185                 for(int i = 0; i < data.size(); i++) {
 186                         data[i].printSequence(out);
 187                 }
 188         }
 189         catch(exception& e) {
 190                 errorOut(e, "SequenceDB", "print");
 191                 exit(1);
 192         }
 193 }
 194
 195 /***********************************************************************/
 196
 197 void SequenceDB::push_back(Sequence newSequence) {
 198         try {
 199                 data.push_back(newSequence);
 200         }
 201         catch(exception& e) {
 202                 errorOut(e, "SequenceDB", "push_back");
 203                 exit(1);
 204         }
 205 }
 206
 207 /***********************************************************************/
 208