1 /* 2 * Copyright (C) 2009 Genome Research Limited 3 * 4 * This program is free software; you can redistribute it and/or 5 * modify it under the terms of the GNU General Public License 6 * as published by the Free Software Foundation; either version 2 7 * of the License, or (at your option) any later version. 8 * 9 * This program is distributed in the hope that it will be useful, 10 * but WITHOUT ANY WARRANTY; without even the implied warranty of 11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 12 * GNU General Public License for more details. 13 * 14 * You should have received a copy of the GNU General Public License 15 * along with this program; if not, write to the Free Software 16 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. 17 * 18 */ 19 package uk.ac.sanger.artemis.circular.digest; 20 21 public class CutSite 22 { 23 private String enzymeName; 24 private int fivePrime; 25 private int threePrime; 26 private int fivePrimeRev; 27 private int threePrimeRev; 28 private boolean forward = false; 29 private boolean highlighted = false; 30 CutSite(final String enzymeName, String fivePrimeStr, String threePrimeStr, String fivePrimeRevStr, String threePrimeRevStr, String strand)31 CutSite(final String enzymeName, 32 String fivePrimeStr, String threePrimeStr, 33 String fivePrimeRevStr, String threePrimeRevStr, 34 String strand) 35 { 36 this.enzymeName = enzymeName; 37 this.fivePrime = Integer.parseInt(fivePrimeStr); 38 this.threePrime = Integer.parseInt(threePrimeStr); 39 if(!fivePrimeRevStr.equals(".")) 40 fivePrimeRev = Integer.parseInt(fivePrimeRevStr); 41 if(!threePrimeRevStr.equals(".")) 42 threePrimeRev = Integer.parseInt(threePrimeRevStr); 43 44 if(strand.equals("+")) 45 forward = true; 46 } 47 getThreePrime()48 public int getThreePrime() 49 { 50 return threePrime; 51 } 52 getFivePrime()53 public int getFivePrime() 54 { 55 return fivePrime; 56 } 57 getFivePrimeRev()58 public int getFivePrimeRev() 59 { 60 return fivePrimeRev; 61 } 62 getThreePrimeRev()63 public int getThreePrimeRev() 64 { 65 return threePrimeRev; 66 } 67 isForward()68 public boolean isForward() 69 { 70 return forward; 71 } 72 isHighlighted()73 public boolean isHighlighted() 74 { 75 return highlighted; 76 } 77 setHighlighted(boolean highlighted)78 public void setHighlighted(boolean highlighted) 79 { 80 this.highlighted = highlighted; 81 } 82 getEnzymeName()83 public String getEnzymeName() 84 { 85 return enzymeName; 86 } 87 } 88