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package jalview.analysis.scoremodels; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.api.analysis.PairwiseScoreModelI; |
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import jalview.api.analysis.ScoreModelI; |
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import jalview.api.analysis.SimilarityParamsI; |
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import jalview.datamodel.AlignmentView; |
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import jalview.math.Matrix; |
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import jalview.math.MatrixI; |
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import jalview.util.Comparison; |
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| 67.3% |
Uncovered Elements: 35 (107) |
Complexity: 34 |
Complexity Density: 0.56 |
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public class PIDModel extends SimilarityScoreModel |
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implements PairwiseScoreModelI |
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{ |
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private static final String NAME = "PID"; |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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public PIDModel()... |
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{ |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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3 |
@Override... |
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public String getName() |
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{ |
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return NAME; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public String getDescription() |
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{ |
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return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public boolean isDNA() |
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{ |
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return true; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public boolean isProtein() |
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{ |
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return true; |
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} |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 3 |
Complexity Density: 0.6 |
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10 |
@Override... |
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public float getPairwiseScore(char c, char d) |
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{ |
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c = toUpper(c); |
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d = toUpper(d); |
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if (c == d && !Comparison.isGap(c)) |
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{ |
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return 1f; |
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} |
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return 0f; |
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} |
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@param |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 3 |
Complexity Density: 1 |
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protected static char toUpper(char c)... |
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{ |
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if ('a' <= c && c <= 'z') |
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{ |
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c += 'A' - 'a'; |
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} |
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return c; |
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} |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
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@Override... |
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public MatrixI findSimilarities(AlignmentView seqData, |
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SimilarityParamsI options) |
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{ |
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String[] seqs = seqData.getSequenceStrings(Comparison.GAP_DASH); |
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MatrixI result = findSimilarities(seqs, options); |
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result.multiply(seqData.getWidth() / 100d); |
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return result; |
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} |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
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0 |
@Override... |
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public MatrixI findDistances(AlignmentView seqData, |
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SimilarityParamsI options) |
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{ |
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MatrixI result = super.findDistances(seqData, options); |
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if (seqData.getWidth() != 0) |
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{ |
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result.multiply(100d / seqData.getWidth()); |
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} |
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return result; |
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} |
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@param |
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@param |
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@return |
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| 0% |
Uncovered Elements: 11 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
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0 |
protected MatrixI findSimilarities(String[] seqs,... |
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SimilarityParamsI options) |
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{ |
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double[][] values = new double[seqs.length][]; |
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for (int row = 0; row < seqs.length; row++) |
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{ |
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values[row] = new double[seqs.length]; |
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for (int col = 0; col < seqs.length; col++) |
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{ |
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double total = computePID(seqs[row], seqs[col], options); |
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values[row][col] = total; |
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} |
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} |
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return new Matrix(values); |
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} |
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@param |
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@param |
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@param |
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@return |
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| 94.7% |
Uncovered Elements: 3 (57) |
Complexity: 16 |
Complexity Density: 0.48 |
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13 |
public static double computePID(String seq1, String seq2,... |
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SimilarityParamsI options) |
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{ |
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int len1 = seq1.length(); |
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int len2 = seq2.length(); |
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int width = Math.max(len1, len2); |
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int total = 0; |
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int divideBy = 0; |
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for (int i = 0; i < width; i++) |
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{ |
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if (i >= len1 || i >= len2) |
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{ |
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if (options.denominateByShortestLength()) |
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{ |
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break; |
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} |
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if (options.includeGaps()) |
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{ |
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divideBy++; |
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} |
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if (options.matchGaps()) |
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{ |
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total++; |
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} |
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continue; |
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} |
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char c1 = seq1.charAt(i); |
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char c2 = seq2.charAt(i); |
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boolean gap1 = Comparison.isGap(c1); |
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boolean gap2 = Comparison.isGap(c2); |
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if (gap1 && gap2) |
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{ |
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if (options.includeGappedColumns()) |
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{ |
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divideBy++; |
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total++; |
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} |
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continue; |
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} |
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if (gap1 || gap2) |
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{ |
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if (options.includeGaps()) |
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{ |
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divideBy++; |
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} |
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if (options.matchGaps()) |
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{ |
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total++; |
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} |
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continue; |
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} |
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40 |
if (toUpper(c1) == toUpper(c2)) |
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{ |
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total++; |
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} |
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divideBy++; |
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} |
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return divideBy == 0 ? 0D : 100D * total / divideBy; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public ScoreModelI getInstance(AlignmentViewPanel avp) |
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{ |
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return this; |
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} |
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} |