import java.awt.Color;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ColourSchemes;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;

/*
 * Example script that registers two new alignment colour schemes
 */

/*
 * Class that defines a colour scheme where odd columns are red,
 * even numbered columns are blue, and gaps are yellow  
 */
class Stripy extends ResidueColourScheme {
    Stripy() { }
    String getSchemeName() { "stripy" }
    Stripy getInstance(AnnotatedCollectionI coll, Map map) { new Stripy() }
    Color findColour(char res, int col, SequenceI seq) 
    {
        if (res == ' ' || res == '-' || res == '.') 
        {
            Color.yellow
         } else if (col % 2 == 0) 
         {
            Color.blue
         } else 
         {
            Color.red
         }
    }
}

/*
 * Class that defines a colour scheme graduated 
 * (approximately) by amino acid weight  
 */
class ByWeight extends ResidueColourScheme {
    int min = 75
    int max = 204
    ByWeight() { }
    boolean isPeptideSpecific() {true}
    String getSchemeName() { "By Weight" }
    ByWeight getInstance(AnnotatedCollectionI coll, Map map) { new ByWeight() }
    Color makeColour(int weight) 
    {
      int i = 255 * (weight - min) / (max - min);
      new Color(i, 0, i);
    }
    Color findColour(char res, int col, SequenceI seq) 
    {
        switch (res) {
          case ' ':
          case '-':
          case '.':
            Color.white
             break
          case 'A':
            makeColour(89)
            break
          case 'R':
            makeColour(174)
            break
          case 'N':
          case 'D':
          case 'B':
          case 'I':
          case 'L':
            makeColour(132)
            break
          case 'C':
            makeColour(121)
            break
          case 'Q':
          case 'E':
          case 'Z':
          case 'K':
          case 'M':
            makeColour(146)
            break
          case 'G':
            makeColour(75)
            break
          case 'H':
            makeColour(155)
            break
          case 'F':
            makeColour(165)
            break
          case 'P':
            makeColour(115)
            break
          case 'S':
            makeColour(105)
            break
          case 'T':
            makeColour(119)
            break
          case 'W':
            makeColour(204)
            break
          case 'Y':
            makeColour(181)
            break
          case 'V':
            makeColour(117)
            break
          default:
            makeColour(150)
        }
      }
}

ColourSchemes.instance.registerColourScheme(new Stripy())
ColourSchemes.instance.registerColourScheme(new ByWeight())