package jalview.schemes;
import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
public class ScoreMatrix extends PairwiseSeqScoreModel
{
}
/**
+ * Answers the score for substituting first char in A1 with first char in A2
*
* @param A1
* @param A2
- * @return score for substituting first char in A1 with first char in A2
+ * @return
*/
public int getPairwiseScore(String A1, String A2)
{
@Override
public int getPairwiseScore(char c, char d)
{
- int pog = 0;
+ int score = 0;
try
{
: ResidueProperties.nucleotideIndex[c];
int b = (type == 0) ? ResidueProperties.aaIndex[d]
: ResidueProperties.nucleotideIndex[d];
-
- /*
- * hack to convert unassigned / unknown (including gap)
- * to index of unknown (X for amino acids, N for nucleotide)
- * TODO: statically assign gap characters to this index?
- */
- if (type == 0)
- {
- if (a == ResidueProperties.maxProteinIndex)
- {
- a = ResidueProperties.aaIndex['X'];
- }
- if (b == ResidueProperties.maxProteinIndex)
- {
- b = ResidueProperties.aaIndex['X'];
- }
- }
- if (type != 0)
- {
- if (a == ResidueProperties.maxNucleotideIndex)
- {
- a = ResidueProperties.nucleotideIndex['N'];
- }
- if (b == ResidueProperties.maxNucleotideIndex)
- {
- b = ResidueProperties.nucleotideIndex['N'];
- }
- }
- pog = matrix[a][b];
+ score = matrix[a][b];
} catch (Exception e)
{
// System.out.println("Unknown residue in " + A1 + " " + A2);
}
- return pog;
+ return score;
}
/**
}
return sb.toString();
}
+
+ /**
+ * Computes an NxN matrix where N is the number of sequences, and entry [i, j]
+ * is sequence[i] pairwise multiplied with sequence[j], as a sum of scores
+ * computed using the current score matrix. For example
+ * <ul>
+ * <li>Sequences:</li>
+ * <li>FKL</li>
+ * <li>R-D</li>
+ * <li>QIA</li>
+ * <li>GWC</li>
+ * <li>Score matrix is BLOSUM62</li>
+ * <li>Gaps treated same as X (unknown)</li>
+ * <li>product [0, 0] = F.F + K.K + L.L = 6 + 5 + 4 = 15</li>
+ * <li>product [1, 1] = R.R + -.- + D.D = 5 + -1 + 6 = 10</li>
+ * <li>product [2, 2] = Q.Q + I.I + A.A = 5 + 4 + 4 = 13</li>
+ * <li>product [3, 3] = G.G + W.W + C.C = 6 + 11 + 9 = 26</li>
+ * <li>product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
+ * <li>and so on</li>
+ * </ul>
+ */
+ public MatrixI computePairwiseScores(String[] seqs)
+ {
+ double[][] values = new double[seqs.length][];
+ for (int row = 0; row < seqs.length; row++)
+ {
+ values[row] = new double[seqs.length];
+ for (int col = 0; col < seqs.length; col++)
+ {
+ int total = 0;
+ int width = Math.min(seqs[row].length(), seqs[col].length());
+ for (int i = 0; i < width; i++)
+ {
+ char c1 = seqs[row].charAt(i);
+ char c2 = seqs[col].charAt(i);
+ int score = getPairwiseScore(c1, c2);
+ total += score;
+ }
+ values[row][col] = total;
+ }
+ }
+ return new Matrix(values);
+ }
}