From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Mon, 13 May 2019 02:11:42 +0000 (-0500)
Subject: VARNA fix for use of _border used by JSComponent (how to avoid this?)
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=425ed088d830fbb91f21782b9890c13cc55ce10a;p=jalview.git

VARNA fix for use of _border used by JSComponent (how to avoid this?)
---

diff --git a/libjs/VARNA-site.zip b/libjs/VARNA-site.zip
index cf1c44c..14655e1 100644
Binary files a/libjs/VARNA-site.zip and b/libjs/VARNA-site.zip differ
diff --git a/srcjar/fr/orsay/lri/varna/VARNAPanel.java b/srcjar/fr/orsay/lri/varna/VARNAPanel.java
index 3ab14b7..4be4e97 100644
--- a/srcjar/fr/orsay/lri/varna/VARNAPanel.java
+++ b/srcjar/fr/orsay/lri/varna/VARNAPanel.java
@@ -2,7 +2,7 @@
  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) 2012  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
+ paper mail : LRI, bat 490 Universit� Paris-Sud 91405 Orsay Cedex France
 
  This file is part of VARNA version 3.9.
  VARNA version 3.9 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
@@ -819,7 +819,7 @@ public class VARNAPanel extends JPanel implements PropertyChangeListener {
 	private boolean _highlightAnnotation = false;
 
 	private int _titleHeight;
-	private Dimension _border = new Dimension(0, 0);
+	private Dimension _myBorder = new Dimension(0, 0);
 
 	private boolean _drawBBox = false;
 	private boolean _drawBorder = false;
@@ -2395,7 +2395,7 @@ public class VARNAPanel extends JPanel implements PropertyChangeListener {
 
 	public void paintComponent(Graphics g, boolean transparentBackground) {
 		if (_premierAffichage) {
-			// _border = new Dimension(0, 0);
+			// _myBorder = new Dimension(0, 0);
 			_translation.x = 0;
 			_translation.y = (int) (-getTitleHeight() / 2.0);
 			_popup.buildPopupMenu();
@@ -2580,7 +2580,7 @@ public class VARNAPanel extends JPanel implements PropertyChangeListener {
 	 *            The new border size
 	 */
 	public void setBorderSize(Dimension b) {
-		_border = b;
+		_myBorder = b;
 	}
 
 	/**
@@ -2590,7 +2590,7 @@ public class VARNAPanel extends JPanel implements PropertyChangeListener {
 	 * @return The border size
 	 */
 	public Dimension getBorderSize() {
-		return _border;
+		return _myBorder;
 	}
 
 	/**
@@ -3553,8 +3553,8 @@ public class VARNAPanel extends JPanel implements PropertyChangeListener {
 	 * @return X-coordinate of the translation
 	 */
 	public int getLeftOffset() {
-		return _border.width
-				+ ((this.getWidth() - 2 * _border.width) - this.getInnerWidth())
+		return _myBorder.width
+				+ ((this.getWidth() - 2 * _myBorder.width) - this.getInnerWidth())
 				/ 2 + _translation.x;
 	}
 
@@ -3565,7 +3565,7 @@ public class VARNAPanel extends JPanel implements PropertyChangeListener {
 	 */
 	public int getInnerWidth() {
 		// Largeur du dessin
-		return (int) Math.round((this.getWidth() - 2 * _border.width)
+		return (int) Math.round((this.getWidth() - 2 * _myBorder.width)
 				* _conf._zoom);
 	}
 
@@ -3575,8 +3575,8 @@ public class VARNAPanel extends JPanel implements PropertyChangeListener {
 	 * @return Y-coordinate of the translation
 	 */
 	public int getTopOffset() {
-		return _border.height
-				+ ((this.getHeight() - 2 * _border.height) - this
+		return _myBorder.height
+				+ ((this.getHeight() - 2 * _myBorder.height) - this
 						.getInnerHeight()) / 2 + _translation.y;
 	}
 
@@ -3588,7 +3588,7 @@ public class VARNAPanel extends JPanel implements PropertyChangeListener {
 	public int getInnerHeight() {
 		// Hauteur du dessin
 		return (int) Math.round((this.getHeight()) * _conf._zoom - 2
-				* _border.height - getTitleHeight());
+				* _myBorder.height - getTitleHeight());
 	}
 
 	/**