Formatted source

[jalview.git] / src / jalview / schemes / ConservationColourScheme.java

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index 8c3f694..bbc0edd 100755 (executable)
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -16,73 +16,87 @@
 * 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
-\r
 package jalview.schemes;\r
-import java.awt.*;\r
+\r
 import jalview.analysis.*;\r
+\r
+import java.awt.*;\r
+\r
 import java.util.Vector;\r
 \r
+\r
 public class ConservationColourScheme extends ResidueColourScheme {\r
-  public Conservation conserve;\r
-  public ColourSchemeI cs;\r
-  public int inc = 30;\r
-\r
-  public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)\r
-  {\r
-    super();\r
-    conserve = cons;\r
-    cs = oldcs;\r
-  }\r
-\r
-  public void setConsensus(Vector consensus)\r
-  {\r
-    this.consensus = consensus;\r
-    if(cs!=null)\r
-      cs.setConsensus(consensus);\r
-  }\r
-\r
-   public Color findColour(String s, int i)\r
-   {\r
-     Color c = Color.white;\r
-     if (cs == null)\r
-       return c;\r
-\r
-     char ch = conserve.getConsSequence().getSequence().charAt(i);\r
-     if (ch == '*' || ch == '+')\r
-     {\r
-       c = cs.findColour(s, i);\r
-     }\r
-     else\r
-     {\r
-       int tmp = 10;\r
-       int t = 0;\r
-       if (!jalview.util.Comparison.isGap(ch))\r
-         t = Integer.parseInt(ch + "");\r
-\r
-       c = cs.findColour(s, i);\r
-\r
-       while (tmp >= t)\r
-       {\r
-         c = lighter(c, inc);\r
-         tmp--;\r
-       }\r
-\r
-     }\r
-\r
-   return c;\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
+    public Conservation conserve;\r
+    public ColourSchemeI cs;\r
+    public int inc = 30;\r
+\r
+    public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs) {\r
+        super();\r
+        conserve = cons;\r
+        cs = oldcs;\r
+    }\r
+\r
+    public void setConsensus(Vector consensus) {\r
+        this.consensus = consensus;\r
+\r
+        if (cs != null) {\r
+            cs.setConsensus(consensus);\r
+        }\r
+    }\r
+\r
+    public Color findColour(String s, int i) {\r
+        Color c = Color.white;\r
+\r
+        if (cs == null) {\r
+            return c;\r
+        }\r
+\r
+        char ch = conserve.getConsSequence().getSequence().charAt(i);\r
+\r
+        if ((ch == '*') || (ch == '+')) {\r
+            c = cs.findColour(s, i);\r
+        } else {\r
+            int tmp = 10;\r
+            int t = 0;\r
+\r
+            if (!jalview.util.Comparison.isGap(ch)) {\r
+                t = Integer.parseInt(ch + "");\r
+            }\r
+\r
+            c = cs.findColour(s, i);\r
+\r
+            while (tmp >= t) {\r
+                c = lighter(c, inc);\r
+                tmp--;\r
+            }\r
+        }\r
+\r
+        return c;\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)) {\r
+            red = red + inc;\r
+        } else {\r
+            red = 255;\r
+        }\r
+\r
+        if (blue < (255 - inc)) {\r
+            blue = blue + inc;\r
+        } else {\r
+            blue = 255;\r
+        }\r
+\r
+        if (green < (255 - inc)) {\r
+            green = green + inc;\r
+        } else {\r
+            green = 255;\r
+        }\r
 \r
+        return new Color(red, green, blue);\r
+    }\r
 }\r