purinepyrimidineIndex['n'] = 2;
}
+ private static final Integer ONE = Integer.valueOf(1);
+
+ private static final Integer ZERO = Integer.valueOf(0);
+
static
{
- aa3Hash.put("ALA", Integer.valueOf(0));
- aa3Hash.put("ARG", Integer.valueOf(1));
+ aa3Hash.put("ALA", ZERO);
+ aa3Hash.put("ARG", ONE);
aa3Hash.put("ASN", Integer.valueOf(2));
aa3Hash.put("ASP", Integer.valueOf(3)); // D
aa3Hash.put("CYS", Integer.valueOf(4));
-3, 3, 0, -1, -4 },
{ -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,
-3, -3, 4, 1, -1, -4 },
- { 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1,
+ { 0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1,
-2, -2, -1, -3, -3, -2, -4 },
{ -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,
-2, 0, 3, -1, -4 },
scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1));
}
- public static final Color[] pidColours = { midBlue,
- new Color(153, 153, 255),
- // Color.lightGray,
- new Color(204, 204, 255), };
-
- public static final float[] pidThresholds = { 80, 60, 40, };
-
public static List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
public static String START = "ATG";
static
{
- hydrophobic.put("I", Integer.valueOf(1));
- hydrophobic.put("L", Integer.valueOf(1));
- hydrophobic.put("V", Integer.valueOf(1));
- hydrophobic.put("C", Integer.valueOf(1));
- hydrophobic.put("A", Integer.valueOf(1));
- hydrophobic.put("G", Integer.valueOf(1));
- hydrophobic.put("M", Integer.valueOf(1));
- hydrophobic.put("F", Integer.valueOf(1));
- hydrophobic.put("Y", Integer.valueOf(1));
- hydrophobic.put("W", Integer.valueOf(1));
- hydrophobic.put("H", Integer.valueOf(1));
- hydrophobic.put("K", Integer.valueOf(1));
- hydrophobic.put("X", Integer.valueOf(1));
- hydrophobic.put("-", Integer.valueOf(1));
- hydrophobic.put("*", Integer.valueOf(1));
- hydrophobic.put("R", Integer.valueOf(0));
- hydrophobic.put("E", Integer.valueOf(0));
- hydrophobic.put("Q", Integer.valueOf(0));
- hydrophobic.put("D", Integer.valueOf(0));
- hydrophobic.put("N", Integer.valueOf(0));
- hydrophobic.put("S", Integer.valueOf(0));
- hydrophobic.put("T", Integer.valueOf(0));
- hydrophobic.put("P", Integer.valueOf(0));
+ hydrophobic.put("I", ONE);
+ hydrophobic.put("L", ONE);
+ hydrophobic.put("V", ONE);
+ hydrophobic.put("C", ONE);
+ hydrophobic.put("A", ONE);
+ hydrophobic.put("G", ONE);
+ hydrophobic.put("M", ONE);
+ hydrophobic.put("F", ONE);
+ hydrophobic.put("Y", ONE);
+ hydrophobic.put("W", ONE);
+ hydrophobic.put("H", ONE);
+ hydrophobic.put("K", ONE);
+ hydrophobic.put("X", ONE);
+ hydrophobic.put("-", ONE);
+ hydrophobic.put("*", ONE);
+ hydrophobic.put("R", ZERO);
+ hydrophobic.put("E", ZERO);
+ hydrophobic.put("Q", ZERO);
+ hydrophobic.put("D", ZERO);
+ hydrophobic.put("N", ZERO);
+ hydrophobic.put("S", ZERO);
+ hydrophobic.put("T", ONE);
+ hydrophobic.put("P", ZERO);
}
static
{
- polar.put("Y", Integer.valueOf(1));
- polar.put("W", Integer.valueOf(1));
- polar.put("H", Integer.valueOf(1));
- polar.put("K", Integer.valueOf(1));
- polar.put("R", Integer.valueOf(1));
- polar.put("E", Integer.valueOf(1));
- polar.put("Q", Integer.valueOf(1));
- polar.put("D", Integer.valueOf(1));
- polar.put("N", Integer.valueOf(1));
- polar.put("S", Integer.valueOf(1));
- polar.put("T", Integer.valueOf(1));
- polar.put("X", Integer.valueOf(1));
- polar.put("-", Integer.valueOf(1));
- polar.put("*", Integer.valueOf(1));
- polar.put("I", Integer.valueOf(0));
- polar.put("L", Integer.valueOf(0));
- polar.put("V", Integer.valueOf(0));
- polar.put("C", Integer.valueOf(0));
- polar.put("A", Integer.valueOf(0));
- polar.put("G", Integer.valueOf(0));
- polar.put("M", Integer.valueOf(0));
- polar.put("F", Integer.valueOf(0));
- polar.put("P", Integer.valueOf(0));
+ polar.put("Y", ONE);
+ polar.put("W", ONE);
+ polar.put("H", ONE);
+ polar.put("K", ONE);
+ polar.put("R", ONE);
+ polar.put("E", ONE);
+ polar.put("Q", ONE);
+ polar.put("D", ONE);
+ polar.put("N", ONE);
+ polar.put("S", ONE);
+ polar.put("T", ONE);
+ polar.put("X", ONE);
+ polar.put("-", ONE);
+ polar.put("*", ONE);
+ polar.put("I", ZERO);
+ polar.put("L", ZERO);
+ polar.put("V", ZERO);
+ polar.put("C", ZERO);
+ polar.put("A", ZERO);
+ polar.put("G", ZERO);
+ polar.put("M", ZERO);
+ polar.put("F", ZERO);
+ polar.put("P", ZERO);
}
static
{
- small.put("I", Integer.valueOf(0));
- small.put("L", Integer.valueOf(0));
- small.put("V", Integer.valueOf(1));
- small.put("C", Integer.valueOf(1));
- small.put("A", Integer.valueOf(1));
- small.put("G", Integer.valueOf(1));
- small.put("M", Integer.valueOf(0));
- small.put("F", Integer.valueOf(0));
- small.put("Y", Integer.valueOf(0));
- small.put("W", Integer.valueOf(0));
- small.put("H", Integer.valueOf(0));
- small.put("K", Integer.valueOf(0));
- small.put("R", Integer.valueOf(0));
- small.put("E", Integer.valueOf(0));
- small.put("Q", Integer.valueOf(0));
- small.put("D", Integer.valueOf(1));
- small.put("N", Integer.valueOf(1));
- small.put("S", Integer.valueOf(1));
- small.put("T", Integer.valueOf(1));
- small.put("P", Integer.valueOf(1));
- small.put("-", Integer.valueOf(1));
- small.put("*", Integer.valueOf(1));
+ small.put("I", ZERO);
+ small.put("L", ZERO);
+ small.put("V", ONE);
+ small.put("C", ONE);
+ small.put("A", ONE);
+ small.put("G", ONE);
+ small.put("M", ZERO);
+ small.put("F", ZERO);
+ small.put("Y", ZERO);
+ small.put("W", ZERO);
+ small.put("H", ZERO);
+ small.put("K", ZERO);
+ small.put("R", ZERO);
+ small.put("E", ZERO);
+ small.put("Q", ZERO);
+ small.put("D", ONE);
+ small.put("N", ONE);
+ small.put("S", ONE);
+ small.put("T", ONE);
+ small.put("P", ONE);
+ small.put("-", ONE);
+ small.put("*", ONE);
}
static
{
- positive.put("I", Integer.valueOf(0));
- positive.put("L", Integer.valueOf(0));
- positive.put("V", Integer.valueOf(0));
- positive.put("C", Integer.valueOf(0));
- positive.put("A", Integer.valueOf(0));
- positive.put("G", Integer.valueOf(0));
- positive.put("M", Integer.valueOf(0));
- positive.put("F", Integer.valueOf(0));
- positive.put("Y", Integer.valueOf(0));
- positive.put("W", Integer.valueOf(0));
- positive.put("H", Integer.valueOf(1));
- positive.put("K", Integer.valueOf(1));
- positive.put("R", Integer.valueOf(1));
- positive.put("E", Integer.valueOf(0));
- positive.put("Q", Integer.valueOf(0));
- positive.put("D", Integer.valueOf(0));
- positive.put("N", Integer.valueOf(0));
- positive.put("S", Integer.valueOf(0));
- positive.put("T", Integer.valueOf(0));
- positive.put("P", Integer.valueOf(0));
- positive.put("-", Integer.valueOf(1));
- positive.put("*", Integer.valueOf(1));
+ positive.put("I", ZERO);
+ positive.put("L", ZERO);
+ positive.put("V", ZERO);
+ positive.put("C", ZERO);
+ positive.put("A", ZERO);
+ positive.put("G", ZERO);
+ positive.put("M", ZERO);
+ positive.put("F", ZERO);
+ positive.put("Y", ZERO);
+ positive.put("W", ZERO);
+ positive.put("H", ONE);
+ positive.put("K", ONE);
+ positive.put("R", ONE);
+ positive.put("E", ZERO);
+ positive.put("Q", ZERO);
+ positive.put("D", ZERO);
+ positive.put("N", ZERO);
+ positive.put("S", ZERO);
+ positive.put("T", ZERO);
+ positive.put("P", ZERO);
+ positive.put("-", ONE);
+ positive.put("*", ONE);
}
static
{
- negative.put("I", Integer.valueOf(0));
- negative.put("L", Integer.valueOf(0));
- negative.put("V", Integer.valueOf(0));
- negative.put("C", Integer.valueOf(0));
- negative.put("A", Integer.valueOf(0));
- negative.put("G", Integer.valueOf(0));
- negative.put("M", Integer.valueOf(0));
- negative.put("F", Integer.valueOf(0));
- negative.put("Y", Integer.valueOf(0));
- negative.put("W", Integer.valueOf(0));
- negative.put("H", Integer.valueOf(0));
- negative.put("K", Integer.valueOf(0));
- negative.put("R", Integer.valueOf(0));
- negative.put("E", Integer.valueOf(1));
- negative.put("Q", Integer.valueOf(0));
- negative.put("D", Integer.valueOf(1));
- negative.put("N", Integer.valueOf(0));
- negative.put("S", Integer.valueOf(0));
- negative.put("T", Integer.valueOf(0));
- negative.put("P", Integer.valueOf(0));
- negative.put("-", Integer.valueOf(1));
- negative.put("*", Integer.valueOf(1));
+ negative.put("I", ZERO);
+ negative.put("L", ZERO);
+ negative.put("V", ZERO);
+ negative.put("C", ZERO);
+ negative.put("A", ZERO);
+ negative.put("G", ZERO);
+ negative.put("M", ZERO);
+ negative.put("F", ZERO);
+ negative.put("Y", ZERO);
+ negative.put("W", ZERO);
+ negative.put("H", ZERO);
+ negative.put("K", ZERO);
+ negative.put("R", ZERO);
+ negative.put("E", ONE);
+ negative.put("Q", ZERO);
+ negative.put("D", ONE);
+ negative.put("N", ZERO);
+ negative.put("S", ZERO);
+ negative.put("T", ZERO);
+ negative.put("P", ZERO);
+ negative.put("-", ONE);
+ negative.put("*", ONE);
}
static
{
- charged.put("I", Integer.valueOf(0));
- charged.put("L", Integer.valueOf(0));
- charged.put("V", Integer.valueOf(0));
- charged.put("C", Integer.valueOf(0));
- charged.put("A", Integer.valueOf(0));
- charged.put("G", Integer.valueOf(0));
- charged.put("M", Integer.valueOf(0));
- charged.put("F", Integer.valueOf(0));
- charged.put("Y", Integer.valueOf(0));
- charged.put("W", Integer.valueOf(0));
- charged.put("H", Integer.valueOf(1));
- charged.put("K", Integer.valueOf(1));
- charged.put("R", Integer.valueOf(1));
- charged.put("E", Integer.valueOf(1));
- charged.put("Q", Integer.valueOf(0));
- charged.put("D", Integer.valueOf(1));
- charged.put("N", Integer.valueOf(0)); // Asparagine is polar but not
+ charged.put("I", ZERO);
+ charged.put("L", ZERO);
+ charged.put("V", ZERO);
+ charged.put("C", ZERO);
+ charged.put("A", ZERO);
+ charged.put("G", ZERO);
+ charged.put("M", ZERO);
+ charged.put("F", ZERO);
+ charged.put("Y", ZERO);
+ charged.put("W", ZERO);
+ charged.put("H", ONE);
+ charged.put("K", ONE);
+ charged.put("R", ONE);
+ charged.put("E", ONE);
+ charged.put("Q", ZERO);
+ charged.put("D", ONE);
+ charged.put("N", ZERO); // Asparagine is polar but not
// charged.
// Alternative would be charged and
// negative (in basic form)?
- charged.put("S", Integer.valueOf(0));
- charged.put("T", Integer.valueOf(0));
- charged.put("P", Integer.valueOf(0));
- charged.put("-", Integer.valueOf(1));
- charged.put("*", Integer.valueOf(1));
+ charged.put("S", ZERO);
+ charged.put("T", ZERO);
+ charged.put("P", ZERO);
+ charged.put("-", ONE);
+ charged.put("*", ONE);
}
static
{
- aromatic.put("I", Integer.valueOf(0));
- aromatic.put("L", Integer.valueOf(0));
- aromatic.put("V", Integer.valueOf(0));
- aromatic.put("C", Integer.valueOf(0));
- aromatic.put("A", Integer.valueOf(0));
- aromatic.put("G", Integer.valueOf(0));
- aromatic.put("M", Integer.valueOf(0));
- aromatic.put("F", Integer.valueOf(1));
- aromatic.put("Y", Integer.valueOf(1));
- aromatic.put("W", Integer.valueOf(1));
- aromatic.put("H", Integer.valueOf(1));
- aromatic.put("K", Integer.valueOf(0));
- aromatic.put("R", Integer.valueOf(0));
- aromatic.put("E", Integer.valueOf(0));
- aromatic.put("Q", Integer.valueOf(0));
- aromatic.put("D", Integer.valueOf(0));
- aromatic.put("N", Integer.valueOf(0));
- aromatic.put("S", Integer.valueOf(0));
- aromatic.put("T", Integer.valueOf(0));
- aromatic.put("P", Integer.valueOf(0));
- aromatic.put("-", Integer.valueOf(1));
- aromatic.put("*", Integer.valueOf(1));
+ aromatic.put("I", ZERO);
+ aromatic.put("L", ZERO);
+ aromatic.put("V", ZERO);
+ aromatic.put("C", ZERO);
+ aromatic.put("A", ZERO);
+ aromatic.put("G", ZERO);
+ aromatic.put("M", ZERO);
+ aromatic.put("F", ONE);
+ aromatic.put("Y", ONE);
+ aromatic.put("W", ONE);
+ aromatic.put("H", ONE);
+ aromatic.put("K", ZERO);
+ aromatic.put("R", ZERO);
+ aromatic.put("E", ZERO);
+ aromatic.put("Q", ZERO);
+ aromatic.put("D", ZERO);
+ aromatic.put("N", ZERO);
+ aromatic.put("S", ZERO);
+ aromatic.put("T", ZERO);
+ aromatic.put("P", ZERO);
+ aromatic.put("-", ONE);
+ aromatic.put("*", ONE);
}
static
{
- aliphatic.put("I", Integer.valueOf(1));
- aliphatic.put("L", Integer.valueOf(1));
- aliphatic.put("V", Integer.valueOf(1));
- aliphatic.put("C", Integer.valueOf(0));
- aliphatic.put("A", Integer.valueOf(0));
- aliphatic.put("G", Integer.valueOf(0));
- aliphatic.put("M", Integer.valueOf(0));
- aliphatic.put("F", Integer.valueOf(0));
- aliphatic.put("Y", Integer.valueOf(0));
- aliphatic.put("W", Integer.valueOf(0));
- aliphatic.put("H", Integer.valueOf(0));
- aliphatic.put("K", Integer.valueOf(0));
- aliphatic.put("R", Integer.valueOf(0));
- aliphatic.put("E", Integer.valueOf(0));
- aliphatic.put("Q", Integer.valueOf(0));
- aliphatic.put("D", Integer.valueOf(0));
- aliphatic.put("N", Integer.valueOf(0));
- aliphatic.put("S", Integer.valueOf(0));
- aliphatic.put("T", Integer.valueOf(0));
- aliphatic.put("P", Integer.valueOf(0));
- aliphatic.put("-", Integer.valueOf(1));
- aliphatic.put("*", Integer.valueOf(1));
+ aliphatic.put("I", ONE);
+ aliphatic.put("L", ONE);
+ aliphatic.put("V", ONE);
+ aliphatic.put("C", ZERO);
+ aliphatic.put("A", ZERO);
+ aliphatic.put("G", ZERO);
+ aliphatic.put("M", ZERO);
+ aliphatic.put("F", ZERO);
+ aliphatic.put("Y", ZERO);
+ aliphatic.put("W", ZERO);
+ aliphatic.put("H", ZERO);
+ aliphatic.put("K", ZERO);
+ aliphatic.put("R", ZERO);
+ aliphatic.put("E", ZERO);
+ aliphatic.put("Q", ZERO);
+ aliphatic.put("D", ZERO);
+ aliphatic.put("N", ZERO);
+ aliphatic.put("S", ZERO);
+ aliphatic.put("T", ZERO);
+ aliphatic.put("P", ZERO);
+ aliphatic.put("-", ONE);
+ aliphatic.put("*", ONE);
}
static
{
- tiny.put("I", Integer.valueOf(0));
- tiny.put("L", Integer.valueOf(0));
- tiny.put("V", Integer.valueOf(0));
- tiny.put("C", Integer.valueOf(0));
- tiny.put("A", Integer.valueOf(1));
- tiny.put("G", Integer.valueOf(1));
- tiny.put("M", Integer.valueOf(0));
- tiny.put("F", Integer.valueOf(0));
- tiny.put("Y", Integer.valueOf(0));
- tiny.put("W", Integer.valueOf(0));
- tiny.put("H", Integer.valueOf(0));
- tiny.put("K", Integer.valueOf(0));
- tiny.put("R", Integer.valueOf(0));
- tiny.put("E", Integer.valueOf(0));
- tiny.put("Q", Integer.valueOf(0));
- tiny.put("D", Integer.valueOf(0));
- tiny.put("N", Integer.valueOf(0));
- tiny.put("S", Integer.valueOf(1));
- tiny.put("T", Integer.valueOf(0));
- tiny.put("P", Integer.valueOf(0));
- tiny.put("-", Integer.valueOf(1));
- tiny.put("*", Integer.valueOf(1));
+ tiny.put("I", ZERO);
+ tiny.put("L", ZERO);
+ tiny.put("V", ZERO);
+ tiny.put("C", ZERO);
+ tiny.put("A", ONE);
+ tiny.put("G", ONE);
+ tiny.put("M", ZERO);
+ tiny.put("F", ZERO);
+ tiny.put("Y", ZERO);
+ tiny.put("W", ZERO);
+ tiny.put("H", ZERO);
+ tiny.put("K", ZERO);
+ tiny.put("R", ZERO);
+ tiny.put("E", ZERO);
+ tiny.put("Q", ZERO);
+ tiny.put("D", ZERO);
+ tiny.put("N", ZERO);
+ tiny.put("S", ONE);
+ tiny.put("T", ZERO);
+ tiny.put("P", ZERO);
+ tiny.put("-", ONE);
+ tiny.put("*", ONE);
}
static
{
- proline.put("I", Integer.valueOf(0));
- proline.put("L", Integer.valueOf(0));
- proline.put("V", Integer.valueOf(0));
- proline.put("C", Integer.valueOf(0));
- proline.put("A", Integer.valueOf(0));
- proline.put("G", Integer.valueOf(0));
- proline.put("M", Integer.valueOf(0));
- proline.put("F", Integer.valueOf(0));
- proline.put("Y", Integer.valueOf(0));
- proline.put("W", Integer.valueOf(0));
- proline.put("H", Integer.valueOf(0));
- proline.put("K", Integer.valueOf(0));
- proline.put("R", Integer.valueOf(0));
- proline.put("E", Integer.valueOf(0));
- proline.put("Q", Integer.valueOf(0));
- proline.put("D", Integer.valueOf(0));
- proline.put("N", Integer.valueOf(0));
- proline.put("S", Integer.valueOf(0));
- proline.put("T", Integer.valueOf(0));
- proline.put("P", Integer.valueOf(1));
- proline.put("-", Integer.valueOf(1));
- proline.put("*", Integer.valueOf(1));
+ proline.put("I", ZERO);
+ proline.put("L", ZERO);
+ proline.put("V", ZERO);
+ proline.put("C", ZERO);
+ proline.put("A", ZERO);
+ proline.put("G", ZERO);
+ proline.put("M", ZERO);
+ proline.put("F", ZERO);
+ proline.put("Y", ZERO);
+ proline.put("W", ZERO);
+ proline.put("H", ZERO);
+ proline.put("K", ZERO);
+ proline.put("R", ZERO);
+ proline.put("E", ZERO);
+ proline.put("Q", ZERO);
+ proline.put("D", ZERO);
+ proline.put("N", ZERO);
+ proline.put("S", ZERO);
+ proline.put("T", ZERO);
+ proline.put("P", ONE);
+ proline.put("-", ONE);
+ proline.put("*", ONE);
}
static
git://source.jalview.org / jalview.git / blobdiff