/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.util.*;
+import jalview.analysis.scoremodels.FeatureScoreModel;
+import jalview.analysis.scoremodels.PIDScoreModel;
+import jalview.api.analysis.ScoreModelI;
-import java.awt.*;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
public class ResidueProperties
{
- public static Hashtable scoreMatrices = new Hashtable();
+ public static Hashtable<String, ScoreModelI> scoreMatrices = new Hashtable();
// Stores residue codes/names and colours and other things
public static final int[] aaIndex; // aaHash version 2.1.1 and below
public static final int[] purinepyrimidineIndex;
- public static final Hashtable aa3Hash = new Hashtable();
+ public static final Map<String, Integer> aa3Hash = new HashMap<String, Integer>();
+
+ public static final Map<String, String> aa2Triplet = new HashMap<String, String>();
- public static final Hashtable aa2Triplet = new Hashtable();
+ public static final Map<String, String> nucleotideName = new HashMap<String, String>();
- public static final Hashtable nucleotideName = new Hashtable();
+ // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
+ public static final Map<String, String> modifications = new HashMap<String, String>();
static
{
// extend subt. matrices
}
+ /**
+ * maximum (gap) index for matrices involving protein alphabet
+ */
+ public final static int maxProteinIndex = 23;
+
+ /**
+ * maximum (gap) index for matrices involving nucleotide alphabet
+ */
+ public final static int maxNucleotideIndex = 10;
+
static
{
nucleotideIndex = new int[255];
aa2Triplet.put("v", "VAL");
}
- public static final String[] aa =
- { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
- "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " " };
+ public static final String[] aa = { "A", "R", "N", "D", "C", "Q", "E",
+ "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B",
+ "Z", "X", "_", "*", ".", " " };
public static final Color midBlue = new Color(100, 100, 255);
scaleColours.addElement(Color.white);
}
- public static final Color[] taylor =
- { new Color(204, 255, 0), // A Greenish-yellowy-yellow
+ public static final Color[] taylor = { new Color(204, 255, 0), // A
+ // Greenish-yellowy-yellow
new Color(0, 0, 255), // R Blueish-bluey-blue
new Color(204, 0, 255), // N Blueish-reddy-blue
new Color(255, 0, 0), // D Reddish-reddy-red
Color.white // .
};
- public static final Color[] nucleotide =
- { new Color(100, 247, 63), // A
+ public static final Color[] nucleotide = { new Color(100, 247, 63), // A
new Color(255, 179, 64), // C
new Color(235, 65, 60), // G
new Color(60, 136, 238), // T
};
// 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
};
// Zappo
- public static final Color[] zappo =
- { Color.pink, // A
+ public static final Color[] zappo = { Color.pink, // A
midBlue, // R
Color.green, // N
Color.red, // D
};
// Dunno where I got these numbers from
- public static final double[] hyd2 =
- { 0.62, // A
+ public static final double[] hyd2 = { 0.62, // A
0.29, // R
-0.90, // N
-0.74, // D
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 helixmax = 1.51;
- public static final double[] strand =
- { 0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,
- 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };
+ public static final double[] strand = { 0.83, 0.93, 0.89, 0.54, 1.19,
+ 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75,
+ 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };
public static final double strandmin = 0.37;
public static final double strandmax = 1.7;
- public static final double[] turn =
- { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,
- 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0,
- 0 };
+ public static final double[] turn = { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98,
+ 0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96,
+ 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0 };
public static final double turnmin = 0.47;
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;
// This is hydropathy index
// Kyte, J., and Doolittle, R.F., J. Mol. Biol.
// 1157, 105-132, 1982
- public static final double[] hyd =
- { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9,
- 1.9, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };
+ public static final double[] hyd = { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5,
+ -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9,
+ -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };
public static final double hydmax = 4.5;
// public static final double hydmax = 1.38;
// public static final double hydmin = -2.53;
- private static final int[][] BLOSUM62 =
- {
+ 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,
{ -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 =
- {
+ 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,
* new Color(60, 136, 238), // U Color.white, // I Color.white, // X
* Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
*/
- static final int[][] DNA =
- {
- { 10, -8, -8, -8, 1, 0, 0, 0, 0, 0, 1 }, // C
- { -8, 10, -8, -8, 1, 0, 0, 0, 0, 0, 1 }, // T
- { -8, -8, 10, -8, 1, 0, 0, 0, 0, 0, 1 }, // A
- { -8, -8, -8, 10, 1, 0, 0, 0, 0, 0, 1 }, // G
- { 1, 1, 1, 1, 10, 0, 0, 0, 0, 0, 1 }, // -
- { 1, 1, 1, 1, 1, 10, 0, 0, 0, 0, 1 }, // -
- { 1, 1, 1, 1, 1, 0, 10, 0, 0, 0, 1 }, // -
- { 1, 1, 1, 1, 1, 0, 0, 10, 0, 0, 1 }, // -
- { 1, 1, 1, 1, 1, 0, 0, 0, 10, 0, 1 }, // -
- { 1, 1, 1, 1, 1, 0, 0, 0, 0, 10, 1 }, // -
+
+ // 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 }, // -
};
/**
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),
+ 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 final float[] pidThresholds = { 80, 60, 40, };
- public static Hashtable codonHash = new Hashtable();
+ public static Map<String, List<String>> codonHash = new HashMap<String, List<String>>();
- public static Vector Lys = new Vector();
+ private static List<String> Lys = new ArrayList<String>();
- public static Vector Asn = new Vector();
+ private static List<String> Asn = new ArrayList<String>();
- public static Vector Gln = new Vector();
+ private static List<String> Gln = new ArrayList<String>();
- public static Vector His = new Vector();
+ private static List<String> His = new ArrayList<String>();
- public static Vector Glu = new Vector();
+ private static List<String> Glu = new ArrayList<String>();
- public static Vector Asp = new Vector();
+ private static List<String> Asp = new ArrayList<String>();
- public static Vector Tyr = new Vector();
+ private static List<String> Tyr = new ArrayList<String>();
- public static Vector Thr = new Vector();
+ private static List<String> Thr = new ArrayList<String>();
- public static Vector Pro = new Vector();
+ private static List<String> Pro = new ArrayList<String>();
- public static Vector Ala = new Vector();
+ private static List<String> Ala = new ArrayList<String>();
- public static Vector Ser = new Vector();
+ private static List<String> Ser = new ArrayList<String>();
- public static Vector Arg = new Vector();
+ private static List<String> Arg = new ArrayList<String>();
- public static Vector Gly = new Vector();
+ private static List<String> Gly = new ArrayList<String>();
- public static Vector Trp = new Vector();
+ private static List<String> Trp = new ArrayList<String>();
- public static Vector Cys = new Vector();
+ private static List<String> Cys = new ArrayList<String>();
- public static Vector Ile = new Vector();
+ private static List<String> Ile = new ArrayList<String>();
- public static Vector Met = new Vector();
+ private static List<String> Met = new ArrayList<String>();
- public static Vector Leu = new Vector();
+ private static List<String> Leu = new ArrayList<String>();
- public static Vector Val = new Vector();
+ private static List<String> Val = new ArrayList<String>();
- public static Vector Phe = new Vector();
+ private static List<String> Phe = new ArrayList<String>();
- public static Vector STOP = new Vector();
+ public static List<String> STOP = new ArrayList<String>();
+
+ public static String START = "ATG";
static
{
codonHash.put("STOP", STOP);
}
- public static Hashtable codonHash2 = new Hashtable();
+ /**
+ * Nucleotide Ambiguity Codes
+ */
+ public static final Map<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
+
+ /**
+ * Codon triplets with additional symbols for unambiguous codons that include
+ * ambiguity codes
+ */
+ public static final Hashtable<String, String> codonHash2 = new Hashtable<String, String>();
+
+ /**
+ * all ambiguity codes for a given base
+ */
+ public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<String, List<String>>();
static
{
+ /*
+ * Ambiguity codes as per http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
+ */
+ ambiguityCodes.put("R", new String[] { "A", "G" });
+ ambiguityCodes.put("Y", new String[] { "T", "C" });
+ ambiguityCodes.put("W", new String[] { "A", "T" });
+ ambiguityCodes.put("S", new String[] { "G", "C" });
+ ambiguityCodes.put("M", new String[] { "A", "C" });
+ ambiguityCodes.put("K", new String[] { "G", "T" });
+ ambiguityCodes.put("H", new String[] { "A", "T", "C" });
+ ambiguityCodes.put("B", new String[] { "G", "T", "C" });
+ ambiguityCodes.put("V", new String[] { "G", "A", "C" });
+ ambiguityCodes.put("D", new String[] { "G", "A", "T" });
+ ambiguityCodes.put("N", new String[] { "G", "A", "T", "C" });
+
+ // Now build codon translation table
codonHash2.put("AAA", "K");
codonHash2.put("AAG", "K");
codonHash2.put("AAC", "N");
codonHash2.put("AAT", "N");
- codonHash2.put("CAA", "E");
- codonHash2.put("CAG", "E");
+ codonHash2.put("CAA", "Q");
+ codonHash2.put("CAG", "Q");
codonHash2.put("CAC", "H");
codonHash2.put("CAT", "H");
- codonHash2.put("GAA", "Q");
- codonHash2.put("GAG", "Q");
+ codonHash2.put("GAA", "E");
+ codonHash2.put("GAG", "E");
codonHash2.put("GAC", "D");
codonHash2.put("GAT", "D");
codonHash2.put("TAT", "Y");
codonHash2.put("ACA", "T");
- codonHash2.put("AAG", "T");
codonHash2.put("ACC", "T");
codonHash2.put("ACT", "T");
+ codonHash2.put("ACG", "T");
codonHash2.put("CCA", "P");
codonHash2.put("CCG", "P");
codonHash2.put("TTC", "F");
codonHash2.put("TTT", "F");
+
+ buildAmbiguityCodonSet();
+ }
+
+ /**
+ * programmatic generation of codons including ambiguity codes
+ */
+ public static void buildAmbiguityCodonSet()
+ {
+ if (_ambiguityCodes.size() > 0)
+ {
+ System.err
+ .println("Ignoring multiple calls to buildAmbiguityCodonSet");
+ return;
+ }
+ // Invert the ambiguity code set
+ for (Map.Entry<String, String[]> acode : ambiguityCodes.entrySet())
+ {
+ for (String r : acode.getValue())
+ {
+ List<String> codesfor = _ambiguityCodes.get(r);
+ if (codesfor == null)
+ {
+ _ambiguityCodes.put(r, codesfor = new ArrayList<String>());
+ }
+ if (!codesfor.contains(acode.getKey()))
+ {
+ codesfor.add(acode.getKey());
+ }
+ else
+ {
+ 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()]);
+ for (String codon : unambcodons)
+ {
+ String residue = codonHash2.get(codon);
+ String acodon[][] = new String[codon.length()][];
+ for (int i = 0, iSize = codon.length(); i < iSize; i++)
+ {
+ String _ac = "" + codon.charAt(i);
+ List<String> acodes = _ambiguityCodes.get(_ac);
+ if (acodes != null)
+ {
+ acodon[i] = acodes.toArray(new String[acodes.size()]);
+ }
+ else
+ {
+ acodon[i] = new String[] {};
+ }
+ }
+ // enumerate all combinations and test for veracity of translation
+ int tpos[] = new int[codon.length()], cpos[] = new int[codon.length()];
+ for (int i = 0; i < tpos.length; i++)
+ {
+ tpos[i] = -1;
+ }
+ tpos[acodon.length - 1] = 0;
+ int ipos, j;
+ while (tpos[0] < acodon[0].length)
+ {
+ // make all codons for this combination
+ char allres[][] = new char[tpos.length][];
+ String _acodon = "";
+ char _anuc;
+ for (ipos = 0; ipos < tpos.length; ipos++)
+ {
+ if (acodon[ipos].length == 0 || tpos[ipos] < 0)
+ {
+ _acodon += codon.charAt(ipos);
+ allres[ipos] = new char[] { codon.charAt(ipos) };
+ }
+ else
+ {
+ _acodon += acodon[ipos][tpos[ipos]];
+ String[] altbase = ambiguityCodes.get(acodon[ipos][tpos[ipos]]);
+ allres[ipos] = new char[altbase.length];
+ j = 0;
+ for (String ab : altbase)
+ {
+ allres[ipos][j++] = ab.charAt(0);
+ }
+ }
+ }
+ // test all codons for this combination
+ for (ipos = 0; ipos < cpos.length; ipos++)
+ {
+ cpos[ipos] = 0;
+ }
+ boolean valid = true;
+ do
+ {
+ String _codon = "";
+ for (j = 0; j < cpos.length; j++)
+ {
+ _codon += allres[j][cpos[j]];
+ }
+ String tr = codonHash2.get(_codon);
+ if (valid = (tr != null && tr.equals(residue)))
+ {
+ // advance to next combination
+ ipos = acodon.length - 1;
+ while (++cpos[ipos] >= allres[ipos].length && ipos > 0)
+ {
+ cpos[ipos] = 0;
+ ipos--;
+ }
+ }
+ } while (valid && cpos[0] < allres[0].length);
+ if (valid)
+ {
+ // Add this to the set of codons we will translate
+ // System.out.println("Adding ambiguity codon: " + _acodon + " for "
+ // + residue);
+ codonHash2.put(_acodon, residue);
+ }
+ else
+ {
+ // System.err.println("Rejecting ambiguity codon: " + _acodon
+ // + " for " + residue);
+ }
+ // next combination
+ ipos = acodon.length - 1;
+ while (++tpos[ipos] >= acodon[ipos].length && ipos > 0)
+ {
+ tpos[ipos] = -1;
+ ipos--;
+ }
+ }
+ }
+
}
static
{
- Lys.addElement("AAA");
- Lys.addElement("AAG");
- Asn.addElement("AAC");
- Asn.addElement("AAT");
-
- Gln.addElement("CAA");
- Gln.addElement("CAG");
- His.addElement("CAC");
- His.addElement("CAT");
-
- Glu.addElement("GAA");
- Glu.addElement("GAG");
- Asp.addElement("GAC");
- Asp.addElement("GAT");
-
- Tyr.addElement("TAC");
- Tyr.addElement("TAT");
-
- Thr.addElement("ACA");
- Thr.addElement("ACG");
- Thr.addElement("ACC");
- Thr.addElement("ACT");
-
- Pro.addElement("CCA");
- Pro.addElement("CCG");
- Pro.addElement("CCC");
- Pro.addElement("CCT");
-
- Ala.addElement("GCA");
- Ala.addElement("GCG");
- Ala.addElement("GCC");
- Ala.addElement("GCT");
-
- Ser.addElement("TCA");
- Ser.addElement("TCG");
- Ser.addElement("TCC");
- Ser.addElement("TCT");
- Ser.addElement("AGC");
- Ser.addElement("AGT");
-
- Arg.addElement("AGA");
- Arg.addElement("AGG");
- Arg.addElement("CGA");
- Arg.addElement("CGG");
- Arg.addElement("CGC");
- Arg.addElement("CGT");
-
- Gly.addElement("GGA");
- Gly.addElement("GGG");
- Gly.addElement("GGC");
- Gly.addElement("GGT");
-
- STOP.addElement("TGA");
- STOP.addElement("TAA");
- STOP.addElement("TAG");
-
- Trp.addElement("TGG");
-
- Cys.addElement("TGC");
- Cys.addElement("TGT");
-
- Ile.addElement("ATA");
- Ile.addElement("ATC");
- Ile.addElement("ATT");
-
- Met.addElement("ATG");
-
- Leu.addElement("CTA");
- Leu.addElement("CTG");
- Leu.addElement("CTC");
- Leu.addElement("CTT");
- Leu.addElement("TTA");
- Leu.addElement("TTG");
-
- Val.addElement("GTA");
- Val.addElement("GTG");
- Val.addElement("GTC");
- Val.addElement("GTT");
-
- Phe.addElement("TTC");
- Phe.addElement("TTT");
+ Lys.add("AAA");
+ Lys.add("AAG");
+ Asn.add("AAC");
+ Asn.add("AAT");
+
+ Gln.add("CAA");
+ Gln.add("CAG");
+ His.add("CAC");
+ His.add("CAT");
+
+ Glu.add("GAA");
+ Glu.add("GAG");
+ Asp.add("GAC");
+ Asp.add("GAT");
+
+ Tyr.add("TAC");
+ Tyr.add("TAT");
+
+ Thr.add("ACA");
+ Thr.add("ACG");
+ Thr.add("ACC");
+ Thr.add("ACT");
+
+ Pro.add("CCA");
+ Pro.add("CCG");
+ Pro.add("CCC");
+ Pro.add("CCT");
+
+ Ala.add("GCA");
+ Ala.add("GCG");
+ Ala.add("GCC");
+ Ala.add("GCT");
+
+ Ser.add("TCA");
+ Ser.add("TCG");
+ Ser.add("TCC");
+ Ser.add("TCT");
+ Ser.add("AGC");
+ Ser.add("AGT");
+
+ Arg.add("AGA");
+ Arg.add("AGG");
+ Arg.add("CGA");
+ Arg.add("CGG");
+ Arg.add("CGC");
+ Arg.add("CGT");
+
+ Gly.add("GGA");
+ Gly.add("GGG");
+ Gly.add("GGC");
+ Gly.add("GGT");
+
+ STOP.add("TGA");
+ STOP.add("TAA");
+ STOP.add("TAG");
+
+ Trp.add("TGG");
+
+ Cys.add("TGC");
+ Cys.add("TGT");
+
+ Ile.add("ATA");
+ Ile.add("ATC");
+ Ile.add("ATT");
+
+ Met.add("ATG");
+
+ Leu.add("CTA");
+ Leu.add("CTG");
+ Leu.add("CTC");
+ Leu.add("CTT");
+ Leu.add("TTA");
+ Leu.add("TTG");
+
+ Val.add("GTA");
+ Val.add("GTG");
+ Val.add("GTC");
+ Val.add("GTT");
+
+ Phe.add("TTC");
+ Phe.add("TTT");
}
// Stores residue codes/names and colours and other things
propHash.put("proline", proline);
propHash.put("polar", polar);
}
+ static
+ {
+ 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;
+ String ic = "";
+ if (aa.length > i)
+ {
+ ic += aa[i];
+ }
+ else
+ {
+ ic = "-";
+ }
+ for (int j = i + 1; j < maxProteinIndex; j++)
+ {
+ String jc = "";
+ if (aa.length > j)
+ {
+ jc += aa[j];
+ }
+ else
+ {
+ jc = "-";
+ }
+ propMatrixF[i][j] = 0;
+ propMatrixPos[i][j] = 0;
+ propMatrixEpos[i][j] = 0;
+ for (Enumeration<String> en = propHash.keys(); en.hasMoreElements();)
+ {
+ String ph = en.nextElement();
+ Map<String, Integer> pph = (Map<String, Integer>) propHash
+ .get(ph);
+ if (pph.get(ic) != null && pph.get(jc) != null)
+ {
+ int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue();
+ // Still working on these definitions.
+ propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0;
+ propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0;
+ propMatrixF[i][j] += icp == jcp ? 2 : 0;
+ propMatrixF[j][i] += icp == jcp ? 2 : 0;
+ propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0;
+ propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0;
+ }
+ }
+ if (maxF < propMatrixF[i][j])
+ {
+ maxF = propMatrixF[i][j];
+ }
+ if (maxP < propMatrixPos[i][j])
+ {
+ maxP = propMatrixPos[i][j];
+ }
+ if (maxEP < propMatrixEpos[i][j])
+ {
+ maxEP = propMatrixEpos[i][j];
+ }
+ }
+ propMatrixF[i][i] = maxF;
+ 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 hyd;
}
- public static Hashtable getAA3Hash()
+ public static Map<String, Integer> getAA3Hash()
{
return aa3Hash;
}
public static String codonTranslate(String lccodon)
{
+ if (false)
+ {
+ return _codonTranslate(lccodon);
+ }
+ String cdn = codonHash2.get(lccodon.toUpperCase());
+ if ("*".equals(cdn))
+ {
+ return "STOP";
+ }
+ return cdn;
+ }
+
+ public static String _codonTranslate(String lccodon)
+ {
String codon = lccodon.toUpperCase();
// all base ambiguity codes yield an 'X' amino acid residue
if (codon.indexOf('X') > -1 || codon.indexOf('N') > -1)
{
return "X";
}
- Enumeration e = codonHash.keys();
-
- while (e.hasMoreElements())
+ for (String key : codonHash.keySet())
{
- String key = (String) e.nextElement();
- Vector tmp = (Vector) codonHash.get(key);
-
- if (tmp.contains(codon))
+ if (codonHash.get(key).contains(codon))
{
return key;
}
public static ScoreMatrix getScoreMatrix(String pwtype)
{
Object val = scoreMatrices.get(pwtype);
- if (val != null)
+ 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];
* Used by getRNASecStrucState
*
*/
- public static Hashtable toRNAssState;
+ public static Hashtable<String, String> toRNAssState;
+
+ public static boolean RNAcloseParen[] = new boolean[255];
static
{
- toRNAssState = new Hashtable();
- toRNAssState.put(")", "S");
- toRNAssState.put("(", "S");
+ toRNAssState = new Hashtable<String, String>();
+ toRNAssState.put(")", "(");
+ toRNAssState.put("(", "(");
+ toRNAssState.put("]", "[");
+ toRNAssState.put("[", "[");
+ toRNAssState.put("{", "{");
+ toRNAssState.put("}", "{");
+ toRNAssState.put(">", ">");
+ toRNAssState.put("<", ">");
+ toRNAssState.put("A", "A");
+ toRNAssState.put("a", "A");
+ toRNAssState.put("B", "B");
+ toRNAssState.put("b", "B");
+ toRNAssState.put("C", "C");
+ toRNAssState.put("c", "C");
+ toRNAssState.put("D", "D");
+ toRNAssState.put("d", "D");
+ toRNAssState.put("E", "E");
+ toRNAssState.put("e", "E");
+ toRNAssState.put("F", "F");
+ toRNAssState.put("f", "F");
+ toRNAssState.put("G", "G");
+ toRNAssState.put("g", "G");
+ toRNAssState.put("H", "H");
+ toRNAssState.put("h", "H");
+ toRNAssState.put("I", "I");
+ toRNAssState.put("i", "I");
+ toRNAssState.put("J", "J");
+ toRNAssState.put("j", "J");
+ toRNAssState.put("K", "K");
+ toRNAssState.put("k", "K");
+ toRNAssState.put("L", "L");
+ toRNAssState.put("l", "L");
+ toRNAssState.put("M", "M");
+ toRNAssState.put("m", "M");
+ toRNAssState.put("N", "N");
+ toRNAssState.put("n", "N");
+ toRNAssState.put("O", "O");
+ toRNAssState.put("o", "O");
+ toRNAssState.put("P", "P");
+ toRNAssState.put("p", "P");
+ toRNAssState.put("Q", "Q");
+ toRNAssState.put("q", "Q");
+ toRNAssState.put("R", "R");
+ toRNAssState.put("r", "R");
+ toRNAssState.put("S", "S");
+ toRNAssState.put("s", "S");
+ toRNAssState.put("T", "T");
+ toRNAssState.put("t", "T");
+ toRNAssState.put("U", "U");
+ toRNAssState.put("u", "U");
+ toRNAssState.put("V", "V");
+ toRNAssState.put("v", "V");
+ toRNAssState.put("W", "W");
+ toRNAssState.put("w", "W");
+ toRNAssState.put("X", "X");
+ toRNAssState.put("x", "X");
+ toRNAssState.put("Y", "Y");
+ toRNAssState.put("y", "Y");
+ toRNAssState.put("Z", "Z");
+ toRNAssState.put("z", "Z");
+ for (int p = 0; p < RNAcloseParen.length; p++)
+ {
+ RNAcloseParen[p] = false;
+ }
+ for (String k : toRNAssState.keySet())
+ {
+ RNAcloseParen[k.charAt(0)] = k.charAt(0) != toRNAssState.get(k)
+ .charAt(0);
+ }
+ }
+
+ static
+ {
+ modifications.put("MSE", "MET"); // Selenomethionine
+ // the rest tbc; from
+ // http://sourceforge.net/p/jmol/mailman/message/12833570/
+ // modifications.put("CSE", "CYS"); // Selenocysteine
+ // modifications.put("PTR", "TYR"); // Phosphotyrosine
+ // modifications.put("SEP", "SER"); // Phosphoserine
+ // modifications.put("HYP", "PRO"); // 4-hydroxyproline
+ // modifications.put("5HP", "GLU"); // Pyroglutamic acid; 5-hydroxyproline
+ // modifications.put("PCA", "GLU"); // Pyroglutamic acid
+ // modifications.put("LYZ", "LYS"); // 5-hydroxylysine
+ }
+
+ public static String getCanonicalAminoAcid(String aa)
+ {
+ String canonical = modifications.get(aa);
+ return canonical == null ? aa : canonical;
}
/**
String ssc = ssstring.substring(i, i + 1);
if (toRNAssState.containsKey(ssc))
{
- ss.append((String) toRNAssState.get(ssc));
+ // valid ss character - so return it
+ ss.append(ssc); // (String) toRNAssState.get(ssc));
}
else
{
return ss.toString();
}
+ public static boolean isCloseParenRNA(char dc)
+ {
+ return RNAcloseParen[dc];
+ }
+
// main method generates perl representation of residue property hash
// / cut here
public static void main(String[] args)
}
System.out.println("};");
}
+
// to here
+
+ /**
+ * Returns a list of residue characters for the specified inputs
+ *
+ * @param nucleotide
+ * @param includeAmbiguous
+ * @return
+ */
+ public static List<String> getResidues(boolean nucleotide,
+ boolean includeAmbiguous)
+ {
+ List<String> result = new ArrayList<String>();
+ if (nucleotide)
+ {
+ for (String nuc : nucleotideName.keySet())
+ {
+ int val = nucleotideIndex[nuc.charAt(0)];
+ if ((!includeAmbiguous && val > 4) || (val >= maxNucleotideIndex))
+ {
+ continue;
+ }
+ nuc = nuc.toUpperCase();
+ if (!result.contains(nuc))
+ {
+ result.add(nuc);
+ }
+ }
+ }
+ else
+ {
+ /*
+ * Peptide
+ */
+ for (String res : aa3Hash.keySet())
+ {
+ int index = aa3Hash.get(res).intValue();
+ if ((!includeAmbiguous && index >= 20) || index >= maxProteinIndex)
+ {
+ continue;
+ }
+ res = res.toUpperCase();
+ if (!result.contains(res))
+ {
+ result.add(res);
+ }
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Returns the single letter code for a three letter code, or '0' if not known
+ *
+ * @param threeLetterCode
+ * not case sensitive
+ * @return
+ */
+ public static char getSingleCharacterCode(String threeLetterCode)
+ {
+ if (threeLetterCode == null)
+ {
+ return '0';
+ }
+ Integer index = ResidueProperties.aa3Hash.get(threeLetterCode
+ .toUpperCase());
+ return index == null ? '0' : aa[index].charAt(0);
+ }
}
git://source.jalview.org / jalview.git / blobdiff