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Viewing changes to uk/ac/babraham/FastQC/Sequence/Sequence.java

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2012-11-20 13:38:32 UTC
  • Revision ID: package-import@ubuntu.com-20121120133832-psohzlsak64g7bdy
Tags: upstream-0.10.1+dfsg
Import upstream version 0.10.1+dfsg

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uk/ac/babraham/FastQC/Sequence/Sequence.java
 
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/**
 
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 * Copyright Copyright 2010-12 Simon Andrews
 
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 *
 
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 *    This file is part of FastQC.
 
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 *
 
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 *    FastQC is free software; you can redistribute it and/or modify
 
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 *    it under the terms of the GNU General Public License as published by
 
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 *    the Free Software Foundation; either version 3 of the License, or
 
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 *    (at your option) any later version.
 
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 *
 
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 *    FastQC is distributed in the hope that it will be useful,
 
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 *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 
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 *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 
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 *    GNU General Public License for more details.
 
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 *
 
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 *    You should have received a copy of the GNU General Public License
 
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 *    along with FastQC; if not, write to the Free Software
 
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 *    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 
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 */
 
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package uk.ac.babraham.FastQC.Sequence;
 
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public class Sequence {
 
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        private String sequence;
 
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        private String quality;
 
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        private String id;
 
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        private SequenceFile file;
 
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        private String colorspace;
 
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        private boolean isFiltered;
 
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        public Sequence (SequenceFile file,String sequence, String quality, String id) {
 
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                this.id = id;
 
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                this.file = file;
 
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                this.sequence = sequence.toUpperCase();
 
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                this.quality = quality;
 
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                this.colorspace = null;
 
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                this.isFiltered = false;
 
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        }
 
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        public Sequence (SequenceFile file,String sequence, String colorspace, String quality, String id) {
 
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                this.id = id;
 
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                this.file = file;
 
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                this.sequence = sequence;
 
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                this.quality = quality;
 
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                this.colorspace = colorspace;
 
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        }
 
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        public void setIsFiltered (boolean isFiltered) {
 
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                this.isFiltered = isFiltered;
 
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        }
 
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        public boolean isFiltered () {
 
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                return isFiltered;
 
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        }
 
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        public SequenceFile file () {
 
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                return file;
 
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        }
 
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        public String getSequence () {
 
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                return sequence;
 
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        }
 
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        public String getColorspace () {
 
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                return colorspace;
 
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        }
 
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        public String getQualityString () {
 
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                return quality;
 
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        }
 
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        public String getID () {
 
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                return id;
 
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        }
 
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}