X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2FnaView%2FConnection.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2FnaView%2FConnection.java;h=bca820bb36d713abacce710d488f7b6e1d6cd5bc;hb=ec8f3cedf60fb1feed6d34de6b49f6bfa78b9dd8;hp=0000000000000000000000000000000000000000;hpb=056dad85a910551cc95e44d451a61f6b8c4dd35d;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/models/naView/Connection.java b/srcjar/fr/orsay/lri/varna/models/naView/Connection.java
new file mode 100644
index 0000000..bca820b
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/models/naView/Connection.java
@@ -0,0 +1,114 @@
+/*
+ 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;
+	}
+}