/*
- * 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 2.7)
+ * Copyright (C) 2011 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.schemes;
-import java.util.*;
-
-import java.awt.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.datamodel.SequenceI;
-import jalview.analysis.*;
+import java.awt.Color;
+import java.util.Hashtable;
/**
* DOCUMENT ME!
boolean conservationColouring = false;
- Color[] colors=null;
+ Color[] colors = null;
int threshold = 0;
* Creates a new ResidueColourScheme object.
*
* @param colors
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param threshold
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public ResidueColourScheme(Color[] colours, int threshold)
{
*/
public Color findColour(char c)
{
- return colors==null ? Color.white : colors[ResidueProperties.aaIndex[c]];
+ return colors == null ? Color.white
+ : colors[ResidueProperties.aaIndex[c]];
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
* DOCUMENT ME!
*
* @param ct
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setThreshold(int ct, boolean ignoreGaps)
{
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param consensus
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setConsensus(Hashtable[] consensus)
{
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/