X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConservationColourScheme.java;h=b47b01a7432fcece099a9cd392f545ab8ffc9de7;hb=1402060fb2ca7b2639ef98da3e22766d01149b16;hp=f8db80314f922dd92d2a31964f7aa620e0c8c78e;hpb=35dd2d23b79efb7440e8463ebe7af3a667f4633c;p=jalview.git

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index f8db803..b47b01a 100755
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -1,103 +1,161 @@
-/* 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.
- */
-
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, 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(Conservation cons, ColourSchemeI oldcs)
-  {
-    super();
-    conserve = cons;
-    cs = oldcs;
-
-  }
-
-
-   public Color findColour(String s, int i, java.util.Vector whatever)
-   {
-     Color c = null;
-     if (colourThreshold > 0 && conserve.getConsSequence() != null)
-     {
-       if (conserve.getConsSequence().getSequence().charAt(i)=='*'
-           || conserve.getConsSequence().getSequence().charAt(i)=='+')
-       {
-         if (byResidue)
-           c = findColour(s, i);
-         else
-           c = Color.red;
-       }
-       else
-       {
-         if (byResidue)
-         {
-
-           int tmp = 10;
-           int t = 0;
-           if (!jalview.util.Comparison.isGap(conserve.getConsSequence().
-                                              getSequence().charAt(i)))
-             t = Integer.parseInt(conserve.getConsSequence().getSequence().
-                                  substring(i, i + 1));
-
-           c = findColour(s, i);
-
-           while (tmp >= t)
-           {
-             //      c = c.darker();
-             c = lighter(c, inc);
-             tmp--;
-           }
-         }
-         else
-           c = Color.yellow;
-       }
-     }
-     return c;
-   }
-
-  public Color findColour(String s, int j) {
-    if(cs!=null)
-      return cs.findColour( s, j, null);
-    else
-      return Color.white;
-  }
-
-
-
-  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);
-  }
+import java.awt.*;
+
+import java.util.Vector;
 
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ConservationColourScheme extends ResidueColourScheme
+{
+    /** DOCUMENT ME!! */
+    public Conservation conserve;
+
+    /** DOCUMENT ME!! */
+    public ColourSchemeI cs;
+
+    /** DOCUMENT ME!! */
+    public int inc = 30;
+
+    /**
+     * Creates a new ConservationColourScheme object.
+     *
+     * @param cons DOCUMENT ME!
+     * @param oldcs DOCUMENT ME!
+     */
+    public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
+    {
+        super();
+        conserve = cons;
+        cs = oldcs;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param consensus DOCUMENT ME!
+     */
+    public void setConsensus(Vector consensus)
+    {
+        super.setConsensus(consensus);
+
+        if (cs != null)
+        {
+            cs.setConsensus(consensus);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    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;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     * @param inc DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    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);
+    }
 }