JAL-3032 adds Java 8 functionality (2/2)

[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
new file mode 100644 (file)
index 0000000..ae08bbd
--- /dev/null
+++ b/src2/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;
+       }
+}