/*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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 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
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");
propHash.put("proline", proline);
propHash.put("polar", polar);
}
+ static
+ {
+ int[][][] propMatrix = new int[3][maxProteinIndex][maxProteinIndex];
+ for (int i=0;i<maxProteinIndex;i++)
+ {
+ String ic="";
+ if (aa.length<i) {
+ ic+=aa[i];
+ }
+ else {ic = "-";}
+ propMatrix[0][i][i]=propHash.size();
+ propMatrix[1][i][i]=propHash.size();
+ propMatrix[2][i][i]=propHash.size();
+ for (int j=i+1;j<maxProteinIndex; j++)
+ {
+ String jc="";
+ if (aa.length<j) {
+ jc+=aa[j];
+ }
+ else {jc = "-";}
+ propMatrix[0][i][j]=0;
+ propMatrix[1][i][j]=0;
+ propMatrix[2][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);
+ propMatrix[0][i][j]+= pph.get(ic).equals(pph.get(jc)) ? pph.get(ic) : -1;
+ propMatrix[1][i][j]+= pph.get(ic).equals(pph.get(jc)) ? 1 : -1;
+ propMatrix[2][i][j]+= pph.get(ic).equals(pph.get(jc)) ? pph.get(ic)*2 : 0;
+ }
+ }
+ }
+
+ scoreMatrices.put("Conservation Pos", new ScoreMatrix("Conservation Pos",propMatrix[0],0));
+ scoreMatrices.put("Conservation Both", new ScoreMatrix("Conservation Both",propMatrix[1],0));
+ scoreMatrices.put("Conservation EnhPos", new ScoreMatrix("Conservation EnhPos",propMatrix[2],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