X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConservationColourScheme.java;h=bbc0edd139adac4ea3605edd14789ce2c2bd5661;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=8c3f694de5f3661289f1b900c1d124c42ccd7163;hpb=5cd8e373c75fb348ecda4d94d8a46468fb92756d;p=jalview.git

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index 8c3f694..bbc0edd 100755
--- 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
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package jalview.schemes;
-import java.awt.*;
+
 import jalview.analysis.*;
+
+import java.awt.*;
+
 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;
-    if(cs!=null)
-      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);
-  }
+    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;
+
+        if (cs != null) {
+            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);
+    }
 }