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

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

diff --git a/src2/fr/orsay/lri/varna/models/naView/Connection.java b/src2/fr/orsay/lri/varna/models/naView/Connection.java
deleted file mode 100644 (file)
index bca820b..0000000
--- a/src2/fr/orsay/lri/varna/models/naView/Connection.java
+++ /dev/null
@@ -1,114 +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;
-
-public class Connection {
-       private Loop loop = new Loop();
-       private Region region = new Region();
-       // Start and end form the 1st base pair of the region.
-       private int start, end;
-       private double xrad, yrad, angle;
-       // True if segment between this connection and the
-       // next must be extruded out of the circle
-       private boolean extruded;
-       // True if the extruded segment must be drawn long.
-       private boolean broken;
-       
-       private boolean _isNull=false;
-
-       public boolean isNull() {
-               return _isNull;
-       }
-
-       public void setNull(boolean isNull) {
-               _isNull = isNull;
-       }
-
-       
-       public Loop getLoop() {
-               return loop;
-       }
-
-       public void setLoop(Loop loop) {
-               this.loop = loop;
-       }
-
-       public Region getRegion() {
-               return region;
-       }
-
-       public void setRegion(Region region) {
-               this.region = region;
-       }
-
-       public int getStart() {
-               return start;
-       }
-
-       public void setStart(int start) {
-               this.start = start;
-       }
-
-       public int getEnd() {
-               return end;
-       }
-
-       public void setEnd(int end) {
-               this.end = end;
-       }
-
-       public double getXrad() {
-               return xrad;
-       }
-
-       public void setXrad(double xrad) {
-               this.xrad = xrad;
-       }
-
-       public double getYrad() {
-               return yrad;
-       }
-
-       public void setYrad(double yrad) {
-               this.yrad = yrad;
-       }
-
-       public double getAngle() {
-               return angle;
-       }
-
-       public void setAngle(double angle) {
-               this.angle = angle;
-       }
-
-       public boolean isExtruded() {
-               return extruded;
-       }
-
-       public void setExtruded(boolean extruded) {
-               this.extruded = extruded;
-       }
-
-       public boolean isBroken() {
-               return broken;
-       }
-
-       public void setBroken(boolean broken) {
-               this.broken = broken;
-       }
-}