-/*
- 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.
- Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
- electronic mail : Yann.Ponty@lri.fr
- paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
-
- This file is part of VARNA version 3.1.
- VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
- as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-
- VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
- without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
- See the GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License along with VARNA version 3.1.
- If not, see http://www.gnu.org/licenses.
- */
-package fr.orsay.lri.varna.models.naView;
-
-import java.util.ArrayList;
-import java.util.Hashtable;
-
-public class Loop {
- private int nconnection;
- private ArrayList<Connection> connections = new ArrayList<Connection>();
- private Hashtable<Integer,Connection> _connections = new Hashtable<Integer,Connection>();
- private int number;
- private int depth;
- private boolean mark;
- private double x, y, radius;
-
- public int getNconnection() {
- return nconnection;
- }
-
- public void setNconnection(int nconnection) {
- this.nconnection = nconnection;
- }
-
- public void setConnection(int i, Connection c)
- {
- Integer n = new Integer(i);
- if (c != null)
- _connections.put(n, c);
- else
- {
- if (!_connections.containsKey(n))
- {
- _connections.put(n, new Connection());
- }
- _connections.get(i).setNull(true);
- }
- }
-
- public Connection getConnection(int i)
- {
- Integer n = new Integer(i);
- if (!_connections.containsKey(n))
- { _connections.put(n, new Connection()); }
- Connection c = _connections.get(n);
- if (c.isNull())
- return null;
- else
- return c;
- }
-
- public void addConnection(int i, Connection c)
- {
- _connections.put(_connections.size(),c);
- }
-
-
- public int getNumber() {
- return number;
- }
-
- public void setNumber(int number) {
- this.number = number;
- }
-
- public int getDepth() {
- return depth;
- }
-
- public void setDepth(int depth) {
- this.depth = depth;
- }
-
- public boolean isMark() {
- return mark;
- }
-
- public void setMark(boolean mark) {
- this.mark = mark;
- }
-
- public double getX() {
- return x;
- }
-
- public void setX(double x) {
- this.x = x;
- }
-
- public double getY() {
- return y;
- }
-
- public void setY(double y) {
- this.y = y;
- }
-
- public double getRadius() {
- return radius;
- }
-
- public void setRadius(double radius) {
- this.radius = radius;
- }
-
- public String toString()
- {
- String result = "Loop:";
- result += " nconnection "+nconnection;
- result += " depth "+depth;
- return result;
- }
-}