package jalview.schemes; import jalview.analysis.SequenceIdMatcher; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.Annotation; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceI; import jalview.io.TCoffeeScoreFile; import java.awt.Color; import java.util.ArrayList; import java.util.IdentityHashMap; import java.util.Map; import java.util.TreeMap; /** * Defines the color score for T-Coffee MSA *
* See http://tcoffee.org
*
*
* @author Paolo Di Tommaso
*
*/
public class TCoffeeColourScheme extends ResidueColourScheme {
static final Color[] colors = {
new Color( 102, 102, 255 ), // #6666FF
new Color( 0, 255, 0), // #00FF00
new Color( 102, 255, 0), // #66FF00
new Color( 204, 255, 0), // #CCFF00
new Color( 255, 255, 0), // #FFFF00
new Color( 255, 204, 0), // #FFCC00
new Color( 255, 153, 0), // #FF9900
new Color( 255, 102, 0), // #FF6600
new Color( 255, 51, 0), // #FF3300
new Color( 255, 34, 0) // #FF2000
};
IdentityHashMap