*/
package jalview.schemes;
-import jalview.analysis.scoremodels.FeatureScoreModel;
-import jalview.analysis.scoremodels.PIDScoreModel;
-import jalview.api.analysis.ScoreModelI;
-
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
public class ResidueProperties
{
- public static Hashtable<String, ScoreModelI> scoreMatrices = new Hashtable<String, ScoreModelI>();
-
// Stores residue codes/names and colours and other things
public static final int[] aaIndex; // aaHash version 2.1.1 and below
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));
};
// Added for PurinePyrimidineColourScheme
- public static final Color[] purinepyrimidine = {
- new Color(255, 131, 250), // A, G, R purines purplish/orchid
+ public static final Color[] purinepyrimidine = { new Color(255, 131, 250), // A,
+ // G,
+ // R
+ // purines
+ // purplish/orchid
new Color(64, 224, 208), // C,U, T, Y pyrimidines turquoise
Color.white, // all other nucleotides
Color.white // Gap
Color.green, // Q
Color.red, // E
Color.magenta, // G
- midBlue,// Color.red, // H
+ midBlue, // Color.red, // H
Color.pink, // I
Color.pink, // L
midBlue, // K
0.0 // X
};
- public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70,
- 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77,
- 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
+ public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11,
+ 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83,
+ 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
public static final double helixmin = 0.57;
public static final double turnmax = 1.56;
- public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3,
- 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5,
- 2.9, 0.4, 0.3, 1.358, 0.00 };
+ public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3,
+ 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4,
+ 0.3, 1.358, 0.00 };
public static final double buriedmin = 0.05;
// public static final double hydmax = 1.38;
// public static final double hydmin = -2.53;
- private static final int[][] BLOSUM62 = {
- { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
- -2, 0, -2, -1, 0, -4 },
- { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3,
- -2, -3, -1, 0, -1, -4 },
- { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2,
- -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,
- -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 },
- { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,
- -2, 1, 4, -1, -4 },
- { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,
- -3, -3, -1, -2, -1, -4 },
- { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2,
- 2, -3, 0, 0, -1, -4 },
- { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,
- -1, 3, -3, -3, -1, -4 },
- { -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,
- -1, 1, -4, -3, -1, -4 },
- { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3,
- -2, -2, 0, 1, -1, -4 },
- { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,
- -1, 1, -3, -1, -1, -4 },
- { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1,
- 3, -1, -3, -3, -1, -4 },
- { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,
- -4, -3, -2, -2, -1, -2, -4 },
- { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,
- -2, 0, 0, 0, -4 },
- { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,
- -2, 0, -1, -1, 0, -4 },
- { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,
- 11, 2, -3, -4, -3, -2, -4 },
- { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2,
- 2, 7, -1, -3, -2, -1, -4 },
- { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,
- -1, 4, -3, -2, -1, -4 },
- { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4,
- -3, -3, 4, 1, -1, -4 },
- { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,
- -2, 1, 4, -1, -4 },
- { 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0,
- -2, -1, -1, -1, -1, -1, -4 },
- { -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
- -4, -4, -4, -4, -4, -4, 1 }, };
-
- static final int[][] PAM250 = {
- { 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3,
- 0, 0, 0, 0, -8 },
- { -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
- -2, -1, 0, -1, -8 },
- { 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,
- 2, 1, 0, -8 },
- { 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4,
- -2, 3, 3, -1, -8 },
- { -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,
- -8, 0, -2, -4, -5, -3, -8 },
- { 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,
- -2, 1, 3, -1, -8 },
- { 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4,
- -2, 3, 3, -1, -8 },
- { 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,
- -1, 0, 0, -1, -8 },
- { -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,
- -2, 1, 2, -1, -8 },
- { -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,
- -1, 4, -2, -2, -1, -8 },
- { -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,
- -1, 2, -3, -3, -1, -8 },
- { -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4,
- -2, 1, 0, -1, -8 },
- { -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4,
- -2, 2, -2, -2, -1, -8 },
- { -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0,
- 7, -1, -4, -5, -2, -8 },
- { 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,
- -1, -1, 0, -1, -8 },
- { 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3,
- -1, 0, 0, 0, -8 },
- { 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3,
- 0, 0, -1, 0, -8 },
- { -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5,
- 17, 0, -6, -5, -6, -4, -8 },
- { -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,
- 10, -2, -3, -4, -2, -8 },
- { 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,
- -2, 4, -2, -2, -1, -8 },
- { 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3,
- -2, 3, 2, -1, -8 },
- { 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4,
- -2, 2, 3, -1, -8 },
- { 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,
- -2, -1, -1, -1, -1, -8 },
- { -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
- -8, -8, -8, -8, -8, -8, 1 }, };
// not currently used
// public static final Map<String, Color> ssHash = new Hashtable<String,
* Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
*/
- // JBPNote: patch matrix for T/U equivalence when working with DNA or RNA.
- // Will equate sequences if working with mixed nucleotide sets.
- // treats T and U identically. R and Y weak equivalence with AG and CTU.
- // N matches any other base weakly
- //
- static final int[][] DNA = { { 10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1 }, // A
- { -8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1 }, // C
- { -8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1 }, // G
- { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // T
- { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // U
- { 1, 1, 1, 1, 1, 10, 0, 0, 0, 1, 1 }, // I
- { 1, 1, 1, 1, 1, 0, 10, 0, 0, 1, 1 }, // X
- { 1, -8, 1, -8, -8, 0, 0, 10, -8, 1, 1 }, // R
- { -8, 1, -8, 1, 1, 0, 0, -8, 10, 1, 1 }, // Y
- { 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1 }, // N
- { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 }, // -
- };
- /**
- * register matrices in list
- */
- static
- {
- scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62", BLOSUM62, 0));
- scoreMatrices.put("PAM250", new ScoreMatrix("PAM250", PAM250, 0));
- 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";
}
else
{
- System.err
- .println("Inconsistency in the IUBMB ambiguity code nomenclature table: collision for "
+ System.err.println(
+ "Inconsistency in the IUBMB ambiguity code nomenclature table: collision for "
+ acode.getKey() + " in residue " + r);
}
}
}
// and programmatically add in the ambiguity codes that yield the same amino
// acid
- String[] unambcodons = codonHash2.keySet().toArray(
- new String[codonHash2.size()]);
+ String[] unambcodons = codonHash2.keySet()
+ .toArray(new String[codonHash2.size()]);
for (String codon : unambcodons)
{
String residue = codonHash2.get(codon);
}
}
// enumerate all combinations and test for veracity of translation
- int tpos[] = new int[codon.length()], cpos[] = new int[codon.length()];
+ int tpos[] = new int[codon.length()],
+ cpos[] = new int[codon.length()];
for (int i = 0; i < tpos.length; i++)
{
tpos[i] = -1;
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.
+ 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
}
static
{
- int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex], propMatrixPos = new int[maxProteinIndex][maxProteinIndex], propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
+ int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex],
+ propMatrixPos = new int[maxProteinIndex][maxProteinIndex],
+ propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
for (int i = 0; i < maxProteinIndex; i++)
{
int maxF = 0, maxP = 0, maxEP = 0;
propMatrixPos[i][i] = maxP;
propMatrixEpos[i][i] = maxEP;
}
- // JAL-1512 comment out physicochemical score matrices for 2.8.1 release
- // scoreMatrices.put("Conservation Pos", new
- // ScoreMatrix("Conservation Pos",propMatrixPos,0));
- // scoreMatrices.put("Conservation Both", new
- // ScoreMatrix("Conservation Both",propMatrixF,0));
- // scoreMatrices.put("Conservation EnhPos", new
- // ScoreMatrix("Conservation EnhPos",propMatrixEpos,0));
- scoreMatrices.put("PID", new PIDScoreModel());
- scoreMatrices.put("Displayed Features", new FeatureScoreModel());
}
private ResidueProperties()
return aa3Hash;
}
- public static int[][] getDNA()
- {
- return ResidueProperties.DNA;
- }
-
- public static int[][] getBLOSUM62()
- {
- return ResidueProperties.BLOSUM62;
- }
-
- public static int getPAM250(String A1, String A2)
- {
- return getPAM250(A1.charAt(0), A2.charAt(0));
- }
-
- public static int getBLOSUM62(char c1, char c2)
- {
- int pog = 0;
-
- try
- {
- int a = aaIndex[c1];
- int b = aaIndex[c2];
-
- pog = ResidueProperties.BLOSUM62[a][b];
- } catch (Exception e)
- {
- // System.out.println("Unknown residue in " + A1 + " " + A2);
- }
-
- return pog;
- }
-
public static String codonTranslate(String lccodon)
{
String cdn = codonHash2.get(lccodon.toUpperCase());
return cdn;
}
- public static int[][] getDefaultPeptideMatrix()
- {
- return ResidueProperties.getBLOSUM62();
- }
-
- public static int[][] getDefaultDnaMatrix()
- {
- return ResidueProperties.getDNA();
- }
-
- /**
- * get a ScoreMatrix based on its string name
- *
- * @param pwtype
- * @return matrix in scoreMatrices with key pwtype or null
- */
- public static ScoreMatrix getScoreMatrix(String pwtype)
- {
- Object val = scoreMatrices.get(pwtype);
- if (val != null && val instanceof ScoreMatrix)
- {
- return (ScoreMatrix) val;
- }
- return null;
- }
-
- /**
- * get a ScoreModel based on its string name
- *
- * @param pwtype
- * @return scoremodel of type pwtype or null
- */
- public static ScoreModelI getScoreModel(String pwtype)
- {
- return scoreMatrices.get(pwtype);
- }
-
- public static int getPAM250(char c, char d)
- {
- int a = aaIndex[c];
- int b = aaIndex[d];
-
- int pog = ResidueProperties.PAM250[a][b];
-
- return pog;
- }
-
public static Hashtable<String, String> toDssp3State;
static
{
{
return '0';
}
- Integer index = ResidueProperties.aa3Hash.get(threeLetterCode
- .toUpperCase());
+ Integer index = ResidueProperties.aa3Hash
+ .get(threeLetterCode.toUpperCase());
return index == null ? '0' : aa[index].charAt(0);
}
}
git://source.jalview.org / jalview.git / blobdiff