/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.
+ * 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 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
}
/**
- * Nucleotide Ambiguity Codes
+ * Nucleotide Ambiguity Codes
*/
- public static final Hashtable<String,String[]> ambiguityCodes=new Hashtable<String,String[]>();
+ public static final Hashtable<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
+
/**
- * Codon triplets with additional symbols for unambiguous codons that include ambiguity codes
+ * Codon triplets with additional symbols for unambiguous codons that include
+ * ambiguity codes
*/
- public static final Hashtable<String,String> codonHash2 = new Hashtable<String,String>();
-
+ 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>>();
-
+ public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<String, List<String>>();
static
{
codonHash2.put("TTC", "F");
codonHash2.put("TTT", "F");
-
+
buildAmbiguityCodonSet();
}
-
+
/**
* programmatic generation of codons including ambiguity codes
*/
}
// 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);
char _anuc;
for (ipos = 0; ipos < tpos.length; ipos++)
{
- if (acodon[ipos].length==0 || tpos[ipos] < 0)
+ if (acodon[ipos].length == 0 || tpos[ipos] < 0)
{
_acodon += codon.charAt(ipos);
allres[ipos] = new char[]
_codon += allres[j][cpos[j]];
}
String tr = codonHash2.get(_codon);
- if (valid = (tr!=null && tr.equals(residue)))
+ if (valid = (tr != null && tr.equals(residue)))
{
// advance to next combination
ipos = acodon.length - 1;
if (valid)
{
// Add this to the set of codons we will translate
-// System.out.println("Adding ambiguity codon: " + _acodon + " for "
-// + residue);
+ // System.out.println("Adding ambiguity codon: " + _acodon + " for "
+ // + residue);
codonHash2.put(_acodon, residue);
}
else
{
-// System.err.println("Rejecting ambiguity codon: " + _acodon
-// + " for " + residue);
+ // System.err.println("Rejecting ambiguity codon: " + _acodon
+ // + " for " + residue);
}
// next combination
ipos = acodon.length - 1;
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()
{
return _codonTranslate(lccodon);
}
String cdn = codonHash2.get(lccodon.toUpperCase());
- if (cdn!=null && cdn.equals("*"))
+ if (cdn != null && cdn.equals("*"))
{
return "STOP";
}
return cdn;
}
+
public static String _codonTranslate(String lccodon)
{
String codon = lccodon.toUpperCase();
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];
public static Hashtable toRNAssState;
static
{
- toRNAssState = new Hashtable();
+ toRNAssState = new Hashtable<String, String>();
toRNAssState.put(")", "(");
toRNAssState.put("(", "(");
toRNAssState.put("]", "[");
toRNAssState.put("c", "C");
toRNAssState.put("D", "D");
toRNAssState.put("d", "D");
- toRNAssState.put("1", "1");
- toRNAssState.put("e", "1");
+ 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("2", "2");
- toRNAssState.put("h", "2");
+ toRNAssState.put("H", "H");
+ toRNAssState.put("h", "H");
toRNAssState.put("I", "I");
toRNAssState.put("i", "I");
toRNAssState.put("J", "J");
toRNAssState.put("y", "Y");
toRNAssState.put("Z", "Z");
toRNAssState.put("z", "Z");
-
+
}
/**
git://source.jalview.org / jalview.git / blobdiff