-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
-\r
-package jalview.schemes;\r
-import java.awt.*;\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-\r
-public class ConservationColourScheme extends ResidueColourScheme {\r
- public Conservation conserve;\r
- boolean byResidue = true;\r
- public ColourSchemeI cs;\r
- public int inc = 30;\r
- int colourThreshold = 7;\r
-\r
- public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)\r
- {\r
- super();\r
- conserve = cons;\r
- cs = oldcs;\r
- }\r
-\r
- public void setColours(DrawableSequence seq, int j) {\r
- Color c = Color.white;\r
- String s = seq.getSequence().substring(j,j+1);\r
-\r
- if (colourThreshold > 0 && conserve.getConsSequence() != null) {\r
- if (fullConservation(j)) {\r
- if (byResidue) {\r
- c = findColour(seq,s,j);\r
- } else {\r
- c = Color.red;\r
- }\r
- } else {\r
- if (byResidue) {\r
-\r
- int tmp = 10;\r
- int t = Integer.parseInt(conserve.getConsSequence().getSequence().substring(j,j+1));\r
- c = findColour(seq,s,j);\r
-\r
- while (tmp >= t) {\r
- // c = c.darker();\r
- c = lighter(c,inc);\r
- tmp--;\r
- }\r
- } else {\r
- c = Color.yellow;\r
- }\r
- }\r
- }\r
-\r
- seq.setColor(c);\r
- }\r
- public Color findColour(String s, int i, java.util.Vector whatever)\r
- {\r
- Color c = null;\r
- if (colourThreshold > 0 && conserve.getConsSequence() != null)\r
- {\r
- if (fullConservation(i)) {\r
- if (byResidue) {\r
- c = findColour(null,s,i);\r
- } else {\r
- c = Color.red;\r
- }\r
- } else {\r
- if (byResidue) {\r
-\r
- int tmp = 10;\r
- int t = 0;\r
- if( !jalview.util.Comparison.isGap( conserve.getConsSequence().getSequence().charAt(i) ))\r
- t=Integer.parseInt(conserve.getConsSequence().getSequence().substring(i,i+1));\r
-\r
- c = findColour(null,s,i);\r
-\r
- while (tmp >= t) {\r
- // c = c.darker();\r
- c = lighter(c,inc);\r
- tmp--;\r
- }\r
- } else {\r
- c = Color.yellow;\r
- }\r
- }\r
- }\r
- return c;\r
- }\r
-\r
- public Color findColour(DrawableSequence seq, String s, int j) {\r
- if(cs!=null)\r
- return cs.findColour( s, -1, null);\r
- else\r
- return Color.white;\r
- }\r
- public boolean fullConservation(int j) {\r
- String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);\r
- if (tmp.equals("*")) return true; else return false;\r
- }\r
- public boolean aboveThreshold(DrawableSequence seq, int j, int threshold) {\r
- String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);\r
-\r
- if (Integer.parseInt(tmp) >= threshold || tmp.equals("*")) {\r
- return true;\r
- } else {\r
- return false;\r
- }\r
- }\r
-\r
- public Color lighter(Color c, int inc) {\r
- int red = c.getRed();\r
- int blue = c.getBlue();\r
- int green = c.getGreen();\r
-\r
- if (red < 255-inc) { red = red +inc;} else {red = 255;}\r
- if (blue < 255-inc) { blue = blue +inc;} else {blue = 255;}\r
- if (green < 255-inc) { green = green +inc;} else {green = 255;}\r
-\r
- return new Color(red,green,blue);\r
- }\r
-\r
-}\r
+/* Jalview - a java multiple alignment editor
+ * Copyright (C) 1998 Michele Clamp
+ *
+ * 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 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.
+ *
+ * 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ */
+
+package jalview.schemes;
+import java.awt.*;
+import jalview.gui.*;
+import jalview.datamodel.*;
+import jalview.analysis.*;
+import java.util.Vector;
+
+public class ConservationColourScheme extends ResidueColourScheme {
+ public Conservation conserve;
+ public ColourSchemeI cs;
+ public int inc = 30;
+
+ public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
+ {
+ super();
+ conserve = cons;
+ cs = oldcs;
+ }
+
+ public void setConsensus(Vector consensus)
+ {
+ this.consensus = consensus;
+ cs.setConsensus(consensus);
+ }
+
+ public Color findColour(String s, int i)
+ {
+ Color c = Color.white;
+ if (cs == null)
+ return c;
+
+ char ch = conserve.getConsSequence().getSequence().charAt(i);
+ if (ch == '*' || ch == '+')
+ {
+ c = cs.findColour(s, i);
+ }
+ else
+ {
+ int tmp = 10;
+ int t = 0;
+ if (!jalview.util.Comparison.isGap(ch))
+ t = Integer.parseInt(ch + "");
+
+ c = cs.findColour(s, i);
+
+ while (tmp >= t)
+ {
+ c = lighter(c, inc);
+ tmp--;
+ }
+
+ }
+
+ return c;
+ }
+
+
+ public Color lighter(Color c, int inc) {
+ int red = c.getRed();
+ int blue = c.getBlue();
+ int green = c.getGreen();
+
+ if (red < 255-inc) { red = red +inc;} else {red = 255;}
+ if (blue < 255-inc) { blue = blue +inc;} else {blue = 255;}
+ if (green < 255-inc) { green = green +inc;} else {green = 255;}
+
+ return new Color(red,green,blue);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff