/*
- * 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 2.8.2)
+ * Copyright (C) 2014 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.
- *
+ *
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.util.*;
+import jalview.analysis.scoremodels.PIDScoreModel;
+import jalview.api.analysis.ScoreModelI;
+import java.util.*;
+import java.util.List;
import java.awt.*;
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
}
/**
- * maximum (gap) index for matrices involving protein alphabet
+ * maximum (gap) index for matrices involving protein alphabet
*/
- public final static int maxProteinIndex=23;
+ public final static int maxProteinIndex = 23;
+
/**
- * maximum (gap) index for matrices involving nucleotide alphabet
+ * maximum (gap) index for matrices involving nucleotide alphabet
*/
- public final static int maxNucleotideIndex=10;
-
+ public final static int maxNucleotideIndex = 10;
+
static
{
nucleotideIndex = new int[255];
// 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 }, // -
+ { 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 =
codonHash.put("STOP", STOP);
}
- public static Hashtable codonHash2 = new Hashtable();
+ /**
+ * Nucleotide Ambiguity Codes
+ */
+ public static final Hashtable<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
{
+ /**
+ * 3.2. Purine (adenine or guanine): R
+ *
+ * R is the symbol previously recommended [1].
+ */
+ ambiguityCodes.put("R", new String[]
+ { "A", "G" });
+
+ /**
+ * 3.3. Pyrimidine (thymine or cytosine): Y
+ *
+ * Y is the symbol previously recommended [1].
+ */
+ ambiguityCodes.put("Y", new String[]
+ { "T", "C" });
+ /**
+ * 3.4. Adenine or thymine: W
+ *
+ * Although several diverse symbols have been used for this pair, (and for
+ * the reciprocal pair G+C), only two symbols have a rational basis, L and
+ * W: L derives from DNA density (light; G+C - heavy - would thus be H); W
+ * derives from the strength of the hydrogen bonding interaction between the
+ * base pairs (weak for A+T: G +C - strong - would thus be S). However, the
+ * system recommended for the three-base series (not-A = B, etc., see below,
+ * section 3.8) rules out H as this would be not-G. W is thus recommended.
+ */
+ ambiguityCodes.put("W", new String[]
+ { "A", "T" });
+ /**
+ * 3.5. Guanine or cytosine: S
+ *
+ * The choice of this symbol is discussed above in section 3.4.
+ */
+ ambiguityCodes.put("S", new String[]
+ { "G", "C" });
+ /**
+ * 3.6. Adenine or cytosine: M
+ *
+ * There are few common features between A and C. The presence of an NH2
+ * group in similar positions on both bases (Fig. 1) makes possible a
+ * logically derived symbol. A and N being ruled out, M (from aMino) is
+ * recommended.
+ *
+ *
+ * Fig. 1. Origin of the symbols M and K The four bases are drawn so as to
+ * show the relationship between adenine and cytosine on the one hand, which
+ * both have aMino groups at the ring position most distant from the point
+ * of attachment to the sugar, and between guanine and thymine on the other,
+ * which both have Keto groups at the corresponding position. The ring atoms
+ * are numbered as recommended [24-26], although for the present purpose
+ * this has the disadvantage of giving discordant numbers to the
+ * corresponding positions.
+ */
+ ambiguityCodes.put("M", new String[]
+ { "A", "C" });
+ /**
+ * 3.7. Guanine or thymine: K By analogy with A and C (section 3.6), both G
+ * and T have Keto groups in similar positions (Fig. 1).
+ */
+ ambiguityCodes.put("K", new String[]
+ { "G", "T" });
+ /**
+ * 3.8. Adenine or thymine or cytosine: H
+ *
+ * Not-G is the most simple means of memorising this combination and symbols
+ * logically related to G were examined. F and H would both be suitable, as
+ * the letters before and after G in the alphabet, but A would have no
+ * equivalent to F. The use of H has historical precedence [2].
+ */
+ ambiguityCodes.put("H", new String[]
+ { "A", "T", "C" });
+ /**
+ * 3.9. Guanine or cytosine or thymine: B
+ *
+ * Not-A as above (section 3.8).
+ */
+ ambiguityCodes.put("B", new String[]
+ { "G", "T", "C" });
+ /**
+ * 3.10. Guanine or adenine or cytosine: V
+ *
+ * Not-T by analogy with not-G (section 3.8) would be U but this is ruled
+ * out to eliminate confusion with uracil. V is the next logical choice.
+ * Note that T and U may in some cases be considered to be synonyms.
+ */
+ ambiguityCodes.put("V", new String[]
+ { "G", "A", "C" });
+ /**
+ * 3.11. Guanine or adenine or thymine: D
+ *
+ * Not-C as above (section 3.8).
+ */
+ ambiguityCodes.put("D", new String[]
+ { "G", "A", "T" });
+ /**
+ * 3.12. Guanine or adenine or thymine or cytosine: N
+ */
+ ambiguityCodes.put("R", 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
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= (Enumeration<String>)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());
+ }
private ResidueProperties()
{
public static String codonTranslate(String lccodon)
{
+ if (false)
+ {
+ return _codonTranslate(lccodon);
+ }
+ String cdn = codonHash2.get(lccodon.toUpperCase());
+ if (cdn!=null && cdn.equals("*"))
+ {
+ 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)
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)
{
public static Hashtable toRNAssState;
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");
+
}
/**
git://source.jalview.org / jalview.git / blobdiff