X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2FnaView%2FLoop.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2FnaView%2FLoop.java;h=ae08bbd7343743b67b2b01c0fc3ec9bea8dca3ae;hb=65740880573a48adc758bec3939ece9d9ae104dd;hp=0000000000000000000000000000000000000000;hpb=71aa78b8a7d54e5aeb6b278310dfd735efb77477;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/models/naView/Loop.java b/srcjar/fr/orsay/lri/varna/models/naView/Loop.java
new file mode 100644
index 0000000..ae08bbd
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/models/naView/Loop.java
@@ -0,0 +1,128 @@
+/*
+ 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;
+	}
+}