Clover icon

jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.analysis.scoremodels

File ScoreMatrix.java

 

Coverage histogram

../../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

76
124
23
1
595
320
67
0.54
5.39
23
2.91

Classes

Class Line # Actions
ScoreMatrix 39 124 67 14
0.9372197493.7%
 

Contributing tests

This file is covered by 119 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.analysis.scoremodels;
22   
23    import jalview.api.AlignmentViewPanel;
24    import jalview.api.analysis.PairwiseScoreModelI;
25    import jalview.api.analysis.ScoreModelI;
26    import jalview.api.analysis.SimilarityParamsI;
27    import jalview.datamodel.AlignmentView;
28    import jalview.math.Matrix;
29    import jalview.math.MatrixI;
30    import jalview.util.Comparison;
31   
32    import java.util.Arrays;
33   
34    /**
35    * A class that models a substitution score matrix for any given alphabet of
36    * symbols. Instances of this class are immutable and thread-safe, so the same
37    * object is returned from calls to getInstance().
38    */
 
39    public class ScoreMatrix extends SimilarityScoreModel
40    implements PairwiseScoreModelI
41    {
42    private static final char GAP_CHARACTER = Comparison.GAP_DASH;
43   
44    /*
45    * an arbitrary score to assign for identity of an unknown symbol
46    * (this is the value on the diagonal in the * column of the NCBI matrix)
47    * (though a case could be made for using the minimum diagonal value)
48    */
49    private static final int UNKNOWN_IDENTITY_SCORE = 1;
50   
51    /*
52    * Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
53    * for pairwise scoring; 2.10.2 uses gap score (last column) in
54    * score matrix (JAL-2397)
55    * Set this flag to true (via Groovy) for 2.10.1 behaviour
56    */
57    private static boolean scoreGapAsAny = false;
58   
59    public static final short UNMAPPED = (short) -1;
60   
61    private static final String BAD_ASCII_ERROR = "Unexpected character %s in getPairwiseScore";
62   
63    private static final int MAX_ASCII = 127;
64   
65    /*
66    * the name of the model as shown in menus
67    * each score model in use should have a unique name
68    */
69    private String name;
70   
71    /*
72    * a description for the model as shown in tooltips
73    */
74    private String description;
75   
76    /*
77    * the characters that the model provides scores for
78    */
79    private char[] symbols;
80   
81    /*
82    * the score matrix; both dimensions must equal the number of symbols
83    * matrix[i][j] is the substitution score for replacing symbols[i] with symbols[j]
84    */
85    private float[][] matrix;
86   
87    /*
88    * quick lookup to convert from an ascii character value to the index
89    * of the corresponding symbol in the score matrix
90    */
91    private short[] symbolIndex;
92   
93    /*
94    * true for Protein Score matrix, false for dna score matrix
95    */
96    private boolean peptide;
97   
98    private float minValue;
99   
100    private float maxValue;
101   
102    /**
103    * Constructor given a name, symbol alphabet, and matrix of scores for pairs
104    * of symbols. The matrix should be square and of the same size as the
105    * alphabet, for example 20x20 for a 20 symbol alphabet.
106    *
107    * @param theName
108    * Unique, human readable name for the matrix
109    * @param alphabet
110    * the symbols to which scores apply
111    * @param values
112    * Pairwise scores indexed according to the symbol alphabet
113    */
 
114  14 toggle public ScoreMatrix(String theName, char[] alphabet, float[][] values)
115    {
116  14 this(theName, null, alphabet, values);
117    }
118   
119    /**
120    * Constructor given a name, description, symbol alphabet, and matrix of
121    * scores for pairs of symbols. The matrix should be square and of the same
122    * size as the alphabet, for example 20x20 for a 20 symbol alphabet.
123    *
124    * @param theName
125    * Unique, human readable name for the matrix
126    * @param theDescription
127    * descriptive display name suitable for use in menus
128    * @param alphabet
129    * the symbols to which scores apply
130    * @param values
131    * Pairwise scores indexed according to the symbol alphabet
132    */
 
133  19 toggle public ScoreMatrix(String theName, String theDescription, char[] alphabet,
134    float[][] values)
135    {
136  19 if (alphabet.length != values.length)
137    {
138  2 throw new IllegalArgumentException(
139    "score matrix size must match alphabet size");
140    }
141  17 for (float[] row : values)
142    {
143  157 if (row.length != alphabet.length)
144    {
145  1 throw new IllegalArgumentException(
146    "score matrix size must be square");
147    }
148    }
149   
150  16 this.matrix = values;
151  16 this.name = theName;
152  16 this.description = theDescription;
153  16 this.symbols = alphabet;
154   
155  16 symbolIndex = buildSymbolIndex(alphabet);
156   
157  16 findMinMax();
158   
159    /*
160    * crude heuristic for now...
161    */
162  16 peptide = alphabet.length >= 20;
163    }
164   
165    /**
166    * Record the minimum and maximum score values
167    */
 
168  16 toggle protected void findMinMax()
169    {
170  16 float min = Float.MAX_VALUE;
171  16 float max = -Float.MAX_VALUE;
172  16 if (matrix != null)
173    {
174  16 for (float[] row : matrix)
175    {
176  155 if (row != null)
177    {
178  155 for (float f : row)
179    {
180  2917 min = Math.min(min, f);
181  2917 max = Math.max(max, f);
182    }
183    }
184    }
185    }
186  16 minValue = min;
187  16 maxValue = max;
188    }
189   
190    /**
191    * Returns an array A where A[i] is the position in the alphabet array of the
192    * character whose value is i. For example if the alphabet is { 'A', 'D', 'X'
193    * } then A['D'] = A[68] = 1.
194    * <p>
195    * Unmapped characters (not in the alphabet) get an index of -1.
196    * <p>
197    * Mappings are added automatically for lower case symbols (for non case
198    * sensitive scoring), unless they are explicitly present in the alphabet (are
199    * scored separately in the score matrix).
200    * <p>
201    * the gap character (space, dash or dot) included in the alphabet (if any) is
202    * recorded in a field
203    *
204    * @param alphabet
205    * @return
206    */
 
207  18 toggle short[] buildSymbolIndex(char[] alphabet)
208    {
209  18 short[] index = new short[MAX_ASCII + 1];
210  18 Arrays.fill(index, UNMAPPED);
211  18 short pos = 0;
212  18 for (char c : alphabet)
213    {
214  165 if (c <= MAX_ASCII)
215    {
216  163 index[c] = pos;
217    }
218   
219    /*
220    * also map lower-case character (unless separately mapped)
221    */
222  165 if (c >= 'A' && c <= 'Z')
223    {
224  148 short lowerCase = (short) (c + ('a' - 'A'));
225  148 if (index[lowerCase] == UNMAPPED)
226    {
227  147 index[lowerCase] = pos;
228    }
229    }
230  165 pos++;
231    }
232  18 return index;
233    }
234   
 
235  1291 toggle @Override
236    public String getName()
237    {
238  1291 return name;
239    }
240   
 
241  4 toggle @Override
242    public String getDescription()
243    {
244  4 return description;
245    }
246   
 
247  3 toggle @Override
248    public boolean isDNA()
249    {
250  3 return !peptide;
251    }
252   
 
253  3 toggle @Override
254    public boolean isProtein()
255    {
256  3 return peptide;
257    }
258   
259    /**
260    * Returns a copy of the score matrix as used in getPairwiseScore. If using
261    * this matrix directly, callers <em>must</em> also call
262    * <code>getMatrixIndex</code> in order to get the matrix index for each
263    * character (symbol).
264    *
265    * @return
266    * @see #getMatrixIndex(char)
267    */
 
268  483 toggle public float[][] getMatrix()
269    {
270  483 float[][] v = new float[matrix.length][matrix.length];
271  12019 for (int i = 0; i < matrix.length; i++)
272    {
273  11536 v[i] = Arrays.copyOf(matrix[i], matrix[i].length);
274    }
275  483 return v;
276    }
277   
278    /**
279    * Answers the matrix index for a given character, or -1 if unmapped in the
280    * matrix. Use this method only if using <code>getMatrix</code> in order to
281    * compute scores directly (without symbol lookup) for efficiency.
282    *
283    * @param c
284    * @return
285    * @see #getMatrix()
286    */
 
287  720541 toggle public int getMatrixIndex(char c)
288    {
289  720546 if (c < symbolIndex.length)
290    {
291  720547 return symbolIndex[c];
292    }
293    else
294    {
295  1 return UNMAPPED;
296    }
297    }
298   
299    /**
300    * Returns the pairwise score for substituting c with d. If either c or d is
301    * an unexpected character, returns 1 for identity (c == d), else the minimum
302    * score value in the matrix.
303    */
 
304  6211636 toggle @Override
305    public float getPairwiseScore(char c, char d)
306    {
307  6211636 if (c >= symbolIndex.length)
308    {
309  1 System.err.println(String.format(BAD_ASCII_ERROR, c));
310  1 return 0;
311    }
312  6211635 if (d >= symbolIndex.length)
313    {
314  2 System.err.println(String.format(BAD_ASCII_ERROR, d));
315  2 return 0;
316    }
317   
318  6211633 int cIndex = symbolIndex[c];
319  6211633 int dIndex = symbolIndex[d];
320  6211633 if (cIndex != UNMAPPED && dIndex != UNMAPPED)
321    {
322  6211588 return matrix[cIndex][dIndex];
323    }
324   
325    /*
326    * one or both symbols not found in the matrix
327    * currently scoring as 1 (for identity) or the minimum
328    * matrix score value (otherwise)
329    * (a case could be made for using minimum row/column value instead)
330    */
331  45 return c == d ? UNKNOWN_IDENTITY_SCORE : getMinimumScore();
332    }
333   
334    /**
335    * pretty print the matrix
336    */
 
337  0 toggle @Override
338    public String toString()
339    {
340  0 return outputMatrix(false);
341    }
342   
343    /**
344    * Print the score matrix, optionally formatted as html, with the alphabet
345    * symbols as column headings and at the start of each row.
346    * <p>
347    * The non-html format should give an output which can be parsed as a score
348    * matrix file
349    *
350    * @param html
351    * @return
352    */
 
353  2 toggle public String outputMatrix(boolean html)
354    {
355  2 StringBuilder sb = new StringBuilder(512);
356   
357    /*
358    * heading row with alphabet
359    */
360  2 if (html)
361    {
362  1 sb.append("<table border=\"1\">");
363  1 sb.append(html ? "<tr><th></th>" : "");
364    }
365    else
366    {
367  1 sb.append("ScoreMatrix ").append(getName()).append("\n");
368    }
369  2 for (char sym : symbols)
370    {
371  26 if (html)
372    {
373  2 sb.append("<th>&nbsp;").append(sym).append("&nbsp;</th>");
374    }
375    else
376    {
377  24 sb.append("\t").append(sym);
378    }
379    }
380  2 sb.append(html ? "</tr>\n" : "\n");
381   
382    /*
383    * table of scores
384    */
385  2 for (char c1 : symbols)
386    {
387  26 if (html)
388    {
389  2 sb.append("<tr><td>");
390    }
391  26 sb.append(c1).append(html ? "</td>" : "");
392  26 for (char c2 : symbols)
393    {
394  580 sb.append(html ? "<td>" : "\t")
395    .append(matrix[symbolIndex[c1]][symbolIndex[c2]])
396  580 .append(html ? "</td>" : "");
397    }
398  26 sb.append(html ? "</tr>\n" : "\n");
399    }
400  2 if (html)
401    {
402  1 sb.append("</table>");
403    }
404  2 return sb.toString();
405    }
406   
407    /**
408    * Answers the number of symbols coded for (also equal to the number of rows
409    * and columns of the score matrix)
410    *
411    * @return
412    */
 
413  483 toggle public int getSize()
414    {
415  483 return symbols.length;
416    }
417   
418    /**
419    * Computes an NxN matrix where N is the number of sequences, and entry [i, j]
420    * is sequence[i] pairwise multiplied with sequence[j], as a sum of scores
421    * computed using the current score matrix. For example
422    * <ul>
423    * <li>Sequences:</li>
424    * <li>FKL</li>
425    * <li>R-D</li>
426    * <li>QIA</li>
427    * <li>GWC</li>
428    * <li>Score matrix is BLOSUM62</li>
429    * <li>Gaps treated same as X (unknown)</li>
430    * <li>product [0, 0] = F.F + K.K + L.L = 6 + 5 + 4 = 15</li>
431    * <li>product [1, 1] = R.R + -.- + D.D = 5 + -1 + 6 = 10</li>
432    * <li>product [2, 2] = Q.Q + I.I + A.A = 5 + 4 + 4 = 13</li>
433    * <li>product [3, 3] = G.G + W.W + C.C = 6 + 11 + 9 = 26</li>
434    * <li>product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
435    * <li>and so on</li>
436    * </ul>
437    * This method is thread-safe.
438    */
 
439  0 toggle @Override
440    public MatrixI findSimilarities(AlignmentView seqstrings,
441    SimilarityParamsI options)
442    {
443  0 char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
444    : GAP_CHARACTER;
445  0 String[] seqs = seqstrings.getSequenceStrings(gapChar);
446  0 return findSimilarities(seqs, options);
447    }
448   
449    /**
450    * Computes pairwise similarities of a set of sequences using the given
451    * parameters
452    *
453    * @param seqs
454    * @param params
455    * @return
456    */
 
457  1 toggle protected MatrixI findSimilarities(String[] seqs,
458    SimilarityParamsI params)
459    {
460  1 double[][] values = new double[seqs.length][];
461  5 for (int row = 0; row < seqs.length; row++)
462    {
463  4 values[row] = new double[seqs.length];
464  20 for (int col = 0; col < seqs.length; col++)
465    {
466  16 double total = computeSimilarity(seqs[row], seqs[col], params);
467  16 values[row][col] = total;
468    }
469    }
470  1 return new Matrix(values);
471    }
472   
473    /**
474    * Calculates the pairwise similarity of two strings using the given
475    * calculation parameters
476    *
477    * @param seq1
478    * @param seq2
479    * @param params
480    * @return
481    */
 
482  32 toggle protected double computeSimilarity(String seq1, String seq2,
483    SimilarityParamsI params)
484    {
485  32 int len1 = seq1.length();
486  32 int len2 = seq2.length();
487  32 double total = 0;
488   
489  32 int width = Math.max(len1, len2);
490  168 for (int i = 0; i < width; i++)
491    {
492  144 if (i >= len1 || i >= len2)
493    {
494    /*
495    * off the end of one sequence; stop if we are only matching
496    * on the shorter sequence length, else treat as trailing gap
497    */
498  16 if (params.denominateByShortestLength())
499    {
500  8 break;
501    }
502    }
503   
504  136 char c1 = i >= len1 ? GAP_CHARACTER : seq1.charAt(i);
505  136 char c2 = i >= len2 ? GAP_CHARACTER : seq2.charAt(i);
506  136 boolean gap1 = Comparison.isGap(c1);
507  136 boolean gap2 = Comparison.isGap(c2);
508   
509  136 if (gap1 && gap2)
510    {
511    /*
512    * gap-gap: include if options say so, else ignore
513    */
514  17 if (!params.includeGappedColumns())
515    {
516  8 continue;
517    }
518    }
519  119 else if (gap1 || gap2)
520    {
521    /*
522    * gap-residue: score if options say so
523    */
524  46 if (!params.includeGaps())
525    {
526  20 continue;
527    }
528    }
529  108 float score = getPairwiseScore(c1, c2);
530  108 total += score;
531    }
532  32 return total;
533    }
534   
535    /**
536    * Answers a hashcode computed from the symbol alphabet and the matrix score
537    * values
538    */
 
539  4 toggle @Override
540    public int hashCode()
541    {
542  4 int hs = Arrays.hashCode(symbols);
543  4 for (float[] row : matrix)
544    {
545  96 hs = hs * 31 + Arrays.hashCode(row);
546    }
547  4 return hs;
548    }
549   
550    /**
551    * Answers true if the argument is a ScoreMatrix with the same symbol alphabet
552    * and score values, else false
553    */
 
554  4 toggle @Override
555    public boolean equals(Object obj)
556    {
557  4 if (!(obj instanceof ScoreMatrix))
558    {
559  1 return false;
560    }
561  3 ScoreMatrix sm = (ScoreMatrix) obj;
562  3 if (Arrays.equals(symbols, sm.symbols)
563    && Arrays.deepEquals(matrix, sm.matrix))
564    {
565  2 return true;
566    }
567  1 return false;
568    }
569   
570    /**
571    * Returns the alphabet the matrix scores for, as a string of characters
572    *
573    * @return
574    */
 
575  1 toggle String getSymbols()
576    {
577  1 return new String(symbols);
578    }
579   
 
580  4431317 toggle public float getMinimumScore()
581    {
582  4431488 return minValue;
583    }
584   
 
585  1 toggle public float getMaximumScore()
586    {
587  1 return maxValue;
588    }
589   
 
590  1 toggle @Override
591    public ScoreModelI getInstance(AlignmentViewPanel avp)
592    {
593  1 return this;
594    }
595    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.