import java.awt.Color; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceCollectionI; /* * Example script that registers two new alignment colour schemes */ /* * Closure that defines a colour scheme where consensus residues are pink, * other residues are red in odd columns and blue in even columns, and * gaps are yellow */ def candy candy = { -> [ /* * name shown in the colour menu */ getSchemeName: { -> 'candy' }, /* * to make a new instance for each alignment view */ getInstance: { AnnotatedCollectionI coll, Map map -> candy() }, /* * method only needed if colour scheme has to recalculate * values when an alignment is modified */ alignmentChanged: { AnnotatedCollectionI coll, Map map -> }, /* * determine colour for a residue at an aligned position of a * sequence, given consensus residue(s) for the column and the * consensus percentage identity score for the column */ findColour: { char res, int col, SequenceI seq, String consensus, float pid -> if (res == ' ' || res == '-' || res == '.') { Color.yellow } else if (consensus.contains(String.valueOf(res))) { Color.pink } else if (col % 2 == 0) { Color.blue } else { Color.red } }, /* * true means applicable to nucleotide or peptide data */ isApplicableTo: {AnnotatedCollectionI coll -> true}, /* * simple colour schemes are those that depend on the residue * only (these are also available to colour structure viewers) */ isSimple: { false } ] as ColourSchemeI } /* * A closure that defines a colour scheme graduated * (approximately) by amino acid weight * here from lightest (G) Blue, to heaviest (W) Red */ def makeColour = { weight -> minWeight = 75 // Glycine maxWeight = 204 // Tryptophan int i = 255 * (weight - minWeight) / (maxWeight - minWeight); new Color(i, 0, 255-i); } def byWeight byWeight = { -> [ getSchemeName: { 'By Weight' }, // this colour scheme is peptide-specific: isApplicableTo: { coll -> !coll.isNucleotide() }, alignmentChanged: { coll, map -> }, getInstance: { coll, map -> byWeight() }, isSimple: { true }, findColour: {res, col, seq, consensus, pid -> 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) } } ] as ColourSchemeI } ColourSchemes.instance.registerColourScheme(candy()) ColourSchemes.instance.registerColourScheme(byWeight())