jalview 2.5 release banner

[jalview.git] / src / jalview / gui / TreeCanvas.java

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 7644673..028552c 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * Jalview 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
@@ -86,13 +85,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * Creates a new TreeCanvas object.
    * 
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param tree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param scroller
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param label
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller)
   {
@@ -110,7 +109,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param sequence
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void treeSelectionChanged(SequenceI sequence)
   {
@@ -135,7 +134,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param tree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setTree(NJTree tree)
   {
@@ -171,19 +170,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param g
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param node
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param chunk
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param scale
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param width
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param offx
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param offy
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void drawNode(Graphics g, SequenceNode node, float chunk,
           float scale, int width, int offx, int offy)
@@ -341,9 +340,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param x
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param y
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -384,7 +383,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param pickBox
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void pickNodes(Rectangle pickBox)
   {
@@ -411,19 +410,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param pickBox
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param node
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param chunk
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param scale
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param width
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param offx
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param offy
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
           float scale, int width, int offx, int offy)
@@ -470,9 +469,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param node
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setColor(SequenceNode node, Color c)
   {
@@ -535,16 +534,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param pg
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pf
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pi
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    * 
    * @throws PrinterException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   public int print(Graphics pg, PageFormat pf, int pi)
           throws PrinterException
@@ -598,7 +597,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param g
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void paintComponent(Graphics g)
   {
@@ -641,7 +640,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param fontSize
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setFont(Font font)
   {
@@ -653,11 +652,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param g1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param width
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param height
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void draw(Graphics g1, int width, int height)
   {
@@ -711,7 +710,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mouseReleased(MouseEvent e)
   {
@@ -721,7 +720,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mouseEntered(MouseEvent e)
   {
@@ -731,7 +730,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mouseExited(MouseEvent e)
   {
@@ -741,7 +740,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mouseClicked(MouseEvent evt)
   {
@@ -815,7 +814,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mousePressed(MouseEvent e)
   {
@@ -938,7 +937,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setShowDistances(boolean state)
   {
@@ -950,7 +949,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setShowBootstrap(boolean state)
   {
@@ -962,7 +961,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setMarkPlaceholders(boolean state)
   {