5 * Created by Thomas Ryabin on 4/13/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "sequencedb.h"
11 #include "sequence.hpp"
13 #include "calculator.h"
16 /***********************************************************************/
18 SequenceDB::SequenceDB() {}
19 /***********************************************************************/
20 //the clear function free's the memory
21 SequenceDB::~SequenceDB() { clear(); }
23 /***********************************************************************/
25 SequenceDB::SequenceDB(int newSize) {
26 data.resize(newSize, Sequence());
29 /***********************************************************************/
31 SequenceDB::SequenceDB(ifstream& filehandle) {
35 while (!filehandle.eof()) {
36 //input sequence info into sequencedb
37 Sequence newSequence(filehandle);
38 data.push_back(newSequence);
40 //takes care of white space
48 errorOut(e, "SequenceDB", "SequenceDB");
52 /*******************************************************************************/
53 string SequenceDB::readName(ifstream& in) {
59 while ((c = in.get()) != EOF) {
60 //if c is not a line return
69 errorOut(e, "SequenceDB", "readName");
74 /*******************************************************************************/
75 string SequenceDB::readSequence(ifstream& in) {
82 //save position in file in case next line is a new name.
86 //if you are at a new name
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
92 }else { sequence += line; }
98 errorOut(e, "SequenceDB", "readSequence");
103 /***********************************************************************/
105 int SequenceDB::getNumSeqs() {
109 /***********************************************************************/
111 void SequenceDB::set(int index, string newUnaligned) {
113 data[index] = Sequence(data[index].getName(), newUnaligned);
115 catch(exception& e) {
116 errorOut(e, "SequenceDB", "set");
121 /***********************************************************************/
123 void SequenceDB::set(int index, Sequence newSeq) {
125 data[index] = newSeq;
127 catch(exception& e) {
128 errorOut(e, "SequenceDB", "set");
133 /***********************************************************************/
135 Sequence SequenceDB::get(int index) {
139 /***********************************************************************/
141 void SequenceDB::resize(int newSize) {
143 data.resize(newSize);
145 catch(exception& e) {
146 errorOut(e, "SequenceDB", "resize");
151 /***********************************************************************/
153 void SequenceDB::clear() {
157 catch(exception& e) {
158 errorOut(e, "SequenceDB", "clear");
163 /***********************************************************************/
165 int SequenceDB::size() {
169 /***********************************************************************/
171 void SequenceDB::print(ostream& out) {
173 for(int i = 0; i < data.size(); i++) {
174 data[i].printSequence(out);
177 catch(exception& e) {
178 errorOut(e, "SequenceDB", "print");
183 /***********************************************************************/
185 void SequenceDB::push_back(Sequence newSequence) {
187 data.push_back(newSequence);
189 catch(exception& e) {
190 errorOut(e, "SequenceDB", "push_back");
195 /***********************************************************************/