-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.schemes;\r
-\r
-import jalview.analysis.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.Vector;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class ConservationColourScheme extends ResidueColourScheme\r
-{\r
- /** DOCUMENT ME!! */\r
- public Conservation conserve;\r
-\r
- /** DOCUMENT ME!! */\r
- public ColourSchemeI cs;\r
-\r
- /** DOCUMENT ME!! */\r
- public int inc = 30;\r
-\r
- /**\r
- * Creates a new ConservationColourScheme object.\r
- *\r
- * @param cons DOCUMENT ME!\r
- * @param oldcs DOCUMENT ME!\r
- */\r
- public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)\r
- {\r
- super();\r
- conserve = cons;\r
- cs = oldcs;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param consensus DOCUMENT ME!\r
- */\r
- public void setConsensus(Vector consensus)\r
- {\r
- super.setConsensus(consensus);\r
-\r
- if (cs != null)\r
- {\r
- cs.setConsensus(consensus);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param i DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(String s, int i)\r
- {\r
- Color c = Color.white;\r
-\r
- if (cs == null)\r
- {\r
- return c;\r
- }\r
-\r
- char ch = conserve.getConsSequence().getSequence().charAt(i);\r
-\r
- if ((ch == '*') || (ch == '+'))\r
- {\r
- c = cs.findColour(s, i);\r
- }\r
- else\r
- {\r
- int tmp = 10;\r
- int t = 0;\r
-\r
- if (!jalview.util.Comparison.isGap(ch))\r
- {\r
- t = Integer.parseInt(ch + "");\r
- }\r
-\r
- c = cs.findColour(s, i);\r
-\r
- while (tmp >= t)\r
- {\r
- c = lighter(c, inc);\r
- tmp--;\r
- }\r
- }\r
-\r
- return c;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param c DOCUMENT ME!\r
- * @param inc DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color lighter(Color c, int inc)\r
- {\r
- int red = c.getRed();\r
- int blue = c.getBlue();\r
- int green = c.getGreen();\r
-\r
- if (red < (255 - inc))\r
- {\r
- red = red + inc;\r
- }\r
- else\r
- {\r
- red = 255;\r
- }\r
-\r
- if (blue < (255 - inc))\r
- {\r
- blue = blue + inc;\r
- }\r
- else\r
- {\r
- blue = 255;\r
- }\r
-\r
- if (green < (255 - inc))\r
- {\r
- green = green + inc;\r
- }\r
- else\r
- {\r
- green = 255;\r
- }\r
-\r
- return new Color(red, green, blue);\r
- }\r
-}\r