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