/*
- * 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;
* Creates a new SeqCanvas object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public SeqCanvas(AlignmentPanel ap)
{
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param startx
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param endx
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param ypos
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param startx
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param endx
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param ypos
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void drawWestScale(Graphics g, int startx, int endx, int ypos)
{
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param startx
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param endx
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param ypos
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void drawEastScale(Graphics g, int startx, int endx, int ypos)
{
* slider adjustment
*
* @param horizontal
- * shift along
+ * shift along
* @param vertical
- * shift up or down in repaint
+ * shift up or down in repaint
*/
public void fastPaint(int horizontal, int vertical)
{
public void paintComponent(Graphics g)
{
BufferedImage lcimg = img; // take reference since other threads may null
- // img and call later.
+ // img and call later.
super.paintComponent(g);
if (lcimg != null
* DOCUMENT ME!
*
* @param cwidth
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param canvasWidth
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param canvasHeight
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param startRes
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawWrappedPanel(Graphics g, int canvasWidth,
int canvasHeight, int startRes)
* DOCUMENT ME!
*
* @param g1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param startRes
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param endRes
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param startSeq
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param endSeq
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param offset
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
int endSeq, int offset)
int blockStart = startRes;
int blockEnd = endRes;
- for (int i = 0; regions!=null && i < regions.size(); i++)
+ for (int i = 0; regions != null && i < regions.size(); i++)
{
int[] region = (int[]) regions.elementAt(i);
int hideStart = region[0];
for (int i = startSeq; i < endSeq; i++)
{
nextSeq = av.alignment.getSequenceAt(i);
- if (nextSeq==null)
+ if (nextSeq == null)
{
- // occasionally, a race condition occurs such that the alignment row is empty
+ // occasionally, a race condition occurs such that the alignment row is
+ // empty
continue;
}
sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
* DOCUMENT ME!
*
* @param results
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void highlightSearchResults(SearchResults results)
{