From 6a4192007f93c030726298295037f6eac97cf4f3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 16 Nov 2004 15:26:19 +0000
Subject: [PATCH] new file

---
 src/jalview/schemes/ConservationColourScheme.java |  138 +++++++++++++++++++++
 1 file changed, 138 insertions(+)
 create mode 100755 src/jalview/schemes/ConservationColourScheme.java

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
new file mode 100755
index 0000000..0eac54b
--- /dev/null
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -0,0 +1,138 @@
+/* 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.*;
+
+public class ConservationColourScheme extends ResidueColourScheme {
+  public Conservation conserve;
+  boolean byResidue = true;
+  public ColourSchemeI cs;
+  public int inc = 30;
+  int colourThreshold =  7;
+
+  public ConservationColourScheme(SequenceGroup sg)
+  {
+    super();
+    this.conserve = sg.getConservation();
+    colourThreshold = 7;
+    this.cs = sg.cs;
+  }
+
+  public void setColours(DrawableSequence seq, int j) {
+    Color c = Color.white;
+    String s = seq.getSequence().substring(j,j+1);
+
+      if (colourThreshold > 0 && conserve.getConsSequence() != null) {
+        if (fullConservation(j)) {
+          if (byResidue) {
+            c = findColour(seq,s,j);
+           } else {
+             c = Color.red;
+           }
+        } else {
+          if (byResidue) {
+
+            int tmp = 10;
+            int t = Integer.parseInt(conserve.getConsSequence().getSequence().substring(j,j+1));
+            c = findColour(seq,s,j);
+
+             while (tmp >= t) {
+              //      c = c.darker();
+              c = lighter(c,inc);
+               tmp--;
+             }
+          } else {
+          c = Color.yellow;
+          }
+        }
+      }
+
+      seq.setColor(c);
+
+  }
+   public Color findColour(SequenceI seq, String s, int i, java.util.Vector whatever)
+   {
+     Color c = null;
+     if (colourThreshold > 0 && conserve.getConsSequence() != null)
+     {
+       if (fullConservation(i)) {
+         if (byResidue) {
+           c = findColour(null,s,i);
+          } else {
+            c = Color.red;
+          }
+       } else {
+         if (byResidue) {
+
+           int tmp = 10;
+           int t = 0;
+           try
+             {t=Integer.parseInt(conserve.getConsSequence().getSequence().substring(i,i+1));}
+             catch(NumberFormatException ex){
+               System.out.println("fix this bug, conserveColourScheme");
+               t=0;
+             }
+           c = findColour(null,s,i);
+
+            while (tmp >= t) {
+             //      c = c.darker();
+             c = lighter(c,inc);
+              tmp--;
+            }
+         } else {
+         c = Color.yellow;
+         }
+       }
+     }
+     return c;
+   }
+
+  public Color findColour(DrawableSequence seq, String s, int j) {
+    return cs.findColour(null, s, -1, null);
+  }
+  public boolean fullConservation(int j) {
+    String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);
+    if (tmp.equals("*")) return true; else return false;
+  }
+  public boolean aboveThreshold(DrawableSequence seq, int j, int threshold) {
+    String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);
+
+    if (Integer.parseInt(tmp) >= threshold || tmp.equals("*")) {
+      return true;
+    } else {
+      return false;
+    }
+  }
+
+  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);
+  }
+
+}
-- 
1.7.10.2