2 VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
3 Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
4 electronic mail : Yann.Ponty@lri.fr
5 paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
7 This file is part of VARNA version 3.1.
8 VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
9 as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
12 without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
13 See the GNU General Public License for more details.
15 You should have received a copy of the GNU General Public License along with VARNA version 3.1.
16 If not, see http://www.gnu.org/licenses.
18 package fr.orsay.lri.varna.models.naView;
20 public class Connection {
21 private Loop loop = new Loop();
22 private Region region = new Region();
23 // Start and end form the 1st base pair of the region.
24 private int start, end;
25 private double xrad, yrad, angle;
26 // True if segment between this connection and the
27 // next must be extruded out of the circle
28 private boolean extruded;
29 // True if the extruded segment must be drawn long.
30 private boolean broken;
32 private boolean _isNull=false;
34 public boolean isNull() {
38 public void setNull(boolean isNull) {
43 public Loop getLoop() {
47 public void setLoop(Loop loop) {
51 public Region getRegion() {
55 public void setRegion(Region region) {
59 public int getStart() {
63 public void setStart(int start) {
71 public void setEnd(int end) {
75 public double getXrad() {
79 public void setXrad(double xrad) {
83 public double getYrad() {
87 public void setYrad(double yrad) {
91 public double getAngle() {
95 public void setAngle(double angle) {
99 public boolean isExtruded() {
103 public void setExtruded(boolean extruded) {
104 this.extruded = extruded;
107 public boolean isBroken() {
111 public void setBroken(boolean broken) {
112 this.broken = broken;