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();  length = 0; samelength = true; }
  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         length = 0; samelength = true;
  28 }
  29
  30 /***********************************************************************/
  31
  32 SequenceDB::SequenceDB(ifstream& filehandle) {
  33         try{
  34                 length = 0; samelength = true;
  35
  36                 //read through file
  37                 while (!filehandle.eof()) {
  38                         //input sequence info into sequencedb
  39                         Sequence newSequence(filehandle);
  40
  41                         if (newSequence.getName() != "") {
  42                                 if (length == 0) { length = newSequence.getAligned().length(); }
  43                                 if (length != newSequence.getAligned().length()) { samelength = false; }
  44                                 data.push_back(newSequence);
  45                         }
  46
  47                         //takes care of white space
  48                         m->gobble(filehandle);
  49                 }
  50
  51                 filehandle.close();
  52
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "SequenceDB", "SequenceDB");
  56                 exit(1);
  57         }
  58 }
  59 /*******************************************************************************/
  60 string SequenceDB::readName(ifstream& in) {
  61         try{
  62                 string name = "";
  63                 int c;
  64                 string temp;
  65
  66                 while ((c = in.get()) != EOF) {
  67                         //if c is not a line return
  68                         if (c != 10) {
  69                                 name += c;
  70                         }else { break;  }
  71                 }
  72
  73                 return name;
  74         }
  75         catch(exception& e) {
  76                 m->errorOut(e, "SequenceDB", "readName");
  77                 exit(1);
  78         }
  79 }
  80
  81 /*******************************************************************************/
  82 string SequenceDB::readSequence(ifstream& in) {
  83         try{
  84                 string sequence = "";
  85                 string line;
  86                 int pos, c;
  87
  88                 while (!in.eof()) {
  89                         //save position in file in case next line is a new name.
  90                         pos = in.tellg();
  91                         line = "";
  92                         in >> line;
  93                         //if you are at a new name
  94                         if (line[0] == '>') {
  95                                 //put file pointer back since you are now at a new name
  96                                 in.seekg(pos, ios::beg);
  97                                 c = in.get();  //because you put it back to a newline char
  98                                 break;
  99                         }else {  sequence += line;      }
 100                 }
 101
 102                 if (length == 0) { length = sequence.length(); }
 103                 if (length != sequence.length()) { samelength = false; }
 104
 105                 return sequence;
 106         }
 107         catch(exception& e) {
 108                 m->errorOut(e, "SequenceDB", "readSequence");
 109                 exit(1);
 110         }
 111 }
 112
 113 /***********************************************************************/
 114
 115 int SequenceDB::getNumSeqs() {
 116         return data.size();
 117 }
 118
 119 /***********************************************************************/
 120
 121 void SequenceDB::set(int index, string newUnaligned) {
 122         try {
 123                 if (length == 0) { length = newUnaligned.length(); }
 124                 if (length != newUnaligned.length()) { samelength = false; }
 125
 126                 data[index] = Sequence(data[index].getName(), newUnaligned);
 127         }
 128         catch(exception& e) {
 129                 m->errorOut(e, "SequenceDB", "set");
 130                 exit(1);
 131         }
 132 }
 133
 134 /***********************************************************************/
 135
 136 void SequenceDB::set(int index, Sequence newSeq) {
 137         try {
 138                 if (length == 0) { length = newSeq.getAligned().length(); }
 139                 if (length != newSeq.getAligned().length()) { samelength = false; }
 140
 141                 data[index] = newSeq;
 142         }
 143         catch(exception& e) {
 144                 m->errorOut(e, "SequenceDB", "set");
 145                 exit(1);
 146         }
 147 }
 148
 149 /***********************************************************************/
 150
 151 Sequence SequenceDB::get(int index) {
 152         return data[index];
 153 }
 154
 155 /***********************************************************************/
 156
 157 void SequenceDB::resize(int newSize) {
 158         try {
 159                 data.resize(newSize);
 160         }
 161         catch(exception& e) {
 162                 m->errorOut(e, "SequenceDB", "resize");
 163                 exit(1);
 164         }
 165 }
 166
 167 /***********************************************************************/
 168
 169 void SequenceDB::clear() {
 170         try {
 171                 data.clear();
 172         }
 173         catch(exception& e) {
 174                 m->errorOut(e, "SequenceDB", "clear");
 175                 exit(1);
 176         }
 177 }
 178
 179 /***********************************************************************/
 180
 181 int SequenceDB::size() {
 182         return data.size();
 183 }
 184
 185 /***********************************************************************/
 186
 187 void SequenceDB::print(ostream& out) {
 188         try {
 189                 for(int i = 0; i < data.size(); i++) {
 190                         data[i].printSequence(out);
 191                 }
 192         }
 193         catch(exception& e) {
 194                 m->errorOut(e, "SequenceDB", "print");
 195                 exit(1);
 196         }
 197 }
 198
 199 /***********************************************************************/
 200
 201 void SequenceDB::push_back(Sequence newSequence) {
 202         try {
 203                 if (length == 0) { length = newSequence.getAligned().length(); }
 204                 if (length != newSequence.getAligned().length()) { samelength = false; }
 205
 206                 data.push_back(newSequence);
 207         }
 208         catch(exception& e) {
 209                 m->errorOut(e, "SequenceDB", "push_back");
 210                 exit(1);
 211         }
 212 }
 213
 214 /***********************************************************************/
 215