JAL-3032 upgrade to Jmol 14.29.17; clearing of src2 directory

[jalview.git] / src2 / fr / orsay / lri / varna / models / naView / Loop.java

diff --git a/src2/fr/orsay/lri/varna/models/naView/Loop.java b/src2/fr/orsay/lri/varna/models/naView/Loop.java
deleted file mode 100644 (file)
index ae08bbd..0000000
--- a/src2/fr/orsay/lri/varna/models/naView/Loop.java
+++ /dev/null
@@ -1,128 +0,0 @@
-/*
- 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;
-       }
-}