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Coverage Report

  1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.io

File TCoffeeScoreFile.java

 

Coverage histogram

../../img/srcFileCovDistChart8.png
21% of files have more coverage

Code metrics

86
165
19
3
656
390
76
0.46
8.68
6.33
4

Classes

Class Line # Actions
TCoffeeScoreFile 92 159 70
0.7198443472%
TCoffeeScoreFile.Header 500 2 3
0.833333383.3%
TCoffeeScoreFile.Block 524 4 3
1.0100%
 

Contributing tests

This file is covered by 11 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.io;
22   
23    import jalview.analysis.SequenceIdMatcher;
24    import jalview.datamodel.AlignmentAnnotation;
25    import jalview.datamodel.AlignmentI;
26    import jalview.datamodel.Annotation;
27    import jalview.datamodel.SequenceI;
28   
29    import java.awt.Color;
30    import java.io.IOException;
31    import java.util.ArrayList;
32    import java.util.HashMap;
33    import java.util.LinkedHashMap;
34    import java.util.List;
35    import java.util.Map;
36    import java.util.regex.Matcher;
37    import java.util.regex.Pattern;
38   
39    /**
40    * A file parser for T-Coffee score ascii format. This file contains the
41    * alignment consensus for each residue in any sequence.
42    * <p>
43    * This file is produced by <code>t_coffee</code> providing the option
44    * <code>-output=score_ascii </code> to the program command line
45    *
46    * An example file is the following
47    *
48    * <pre>
49    * T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
50    * Cedric Notredame
51    * CPU TIME:0 sec.
52    * SCORE=90
53    * *
54    * BAD AVG GOOD
55    * *
56    * 1PHT : 89
57    * 1BB9 : 90
58    * 1UHC : 94
59    * 1YCS : 94
60    * 1OOT : 93
61    * 1ABO : 94
62    * 1FYN : 94
63    * 1QCF : 94
64    * cons : 90
65    *
66    * 1PHT 999999999999999999999999998762112222543211112134
67    * 1BB9 99999999999999999999999999987-------4322----2234
68    * 1UHC 99999999999999999999999999987-------5321----2246
69    * 1YCS 99999999999999999999999999986-------4321----1-35
70    * 1OOT 999999999999999999999999999861-------3------1135
71    * 1ABO 99999999999999999999999999986-------422-------34
72    * 1FYN 99999999999999999999999999985-------32--------35
73    * 1QCF 99999999999999999999999999974-------2---------24
74    * cons 999999999999999999999999999851000110321100001134
75    *
76    *
77    * 1PHT ----------5666642367889999999999889
78    * 1BB9 1111111111676653-355679999999999889
79    * 1UHC ----------788774--66789999999999889
80    * 1YCS ----------78777--356789999999999889
81    * 1OOT ----------78877--356789999999997-67
82    * 1ABO ----------687774--56779999999999889
83    * 1FYN ----------6888842356789999999999889
84    * 1QCF ----------6878742356789999999999889
85    * cons 00100000006877641356789999999999889
86    * </pre>
87    *
88    *
89    * @author Paolo Di Tommaso
90    *
91    */
 
92    public class TCoffeeScoreFile extends AlignFile
93    {
94   
95    /**
96    * TCOFFEE score colourscheme
97    */
98    static final Color[] colors = { new Color(102, 102, 255), // 0: lilac #6666FF
99    new Color(0, 255, 0), // 1: green #00FF00
100    new Color(102, 255, 0), // 2: lime green #66FF00
101    new Color(204, 255, 0), // 3: greeny yellow #CCFF00
102    new Color(255, 255, 0), // 4: yellow #FFFF00
103    new Color(255, 204, 0), // 5: orange #FFCC00
104    new Color(255, 153, 0), // 6: deep orange #FF9900
105    new Color(255, 102, 0), // 7: ochre #FF6600
106    new Color(255, 51, 0), // 8: red #FF3300
107    new Color(255, 34, 0) // 9: redder #FF2000
108    };
109   
110    public final static String TCOFFEE_SCORE = "TCoffeeScore";
111   
112    static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
113    .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
114   
115    /** The {@link Header} structure holder */
116    Header header;
117   
118    /**
119    * Holds the consensues values for each sequences. It uses a LinkedHashMap to
120    * maintaint the insertion order.
121    */
122    LinkedHashMap<String, StringBuilder> scores;
123   
124    Integer fWidth;
125   
 
126  10 toggle public TCoffeeScoreFile(Object inFile, DataSourceType fileSourceType)
127    throws IOException
128    {
129    // BH 2018 allows File or String
130  10 super(inFile, fileSourceType);
131   
132    }
133   
 
134  0 toggle public TCoffeeScoreFile(FileParse source) throws IOException
135    {
136  0 super(source);
137    }
138   
139    /**
140    * Parse the provided reader for the T-Coffee scores file format
141    *
142    * @param reader
143    * public static TCoffeeScoreFile load(Reader reader) {
144    *
145    * try { BufferedReader in = (BufferedReader) (reader instanceof
146    * BufferedReader ? reader : new BufferedReader(reader));
147    * TCoffeeScoreFile result = new TCoffeeScoreFile();
148    * result.doParsing(in); return result.header != null &&
149    * result.scores != null ? result : null; } catch( Exception e) {
150    * throw new RuntimeException(e); } }
151    */
152   
153    /**
154    * @return The 'height' of the score matrix i.e. the numbers of score rows
155    * that should matches the number of sequences in the alignment
156    */
 
157  3 toggle public int getHeight()
158    {
159    // the last entry will always be the 'global' alingment consensus scores, so
160    // it is removed
161    // from the 'height' count to make this value compatible with the number of
162    // sequences in the MSA
163  3 return scores != null && scores.size() > 0 ? scores.size() - 1 : 0;
164    }
165   
166    /**
167    * @return The 'width' of the score matrix i.e. the number of columns. Since
168    * the score value are supposed to be calculated for an 'aligned' MSA,
169    * all the entries have to have the same width.
170    */
 
171  3 toggle public int getWidth()
172    {
173  3 return fWidth != null ? fWidth : 0;
174    }
175   
176    /**
177    * Get the string of score values for the specified seqeunce ID.
178    *
179    * @param id
180    * The sequence ID
181    * @return The scores as a string of values e.g. {@code 99999987-------432}.
182    * It return an empty string when the specified ID is missing.
183    */
 
184  9 toggle public String getScoresFor(String id)
185    {
186  9 return scores != null && scores.containsKey(id)
187    ? scores.get(id).toString()
188    : "";
189    }
190   
191    /**
192    * @return The list of score string as a {@link List} object, in the same
193    * ordeer of the insertion i.e. in the MSA
194    */
 
195  1 toggle public List<String> getScoresList()
196    {
197  1 if (scores == null)
198    {
199  0 return null;
200    }
201  1 List<String> result = new ArrayList<String>(scores.size());
202  1 for (Map.Entry<String, StringBuilder> it : scores.entrySet())
203    {
204  9 result.add(it.getValue().toString());
205    }
206   
207  1 return result;
208    }
209   
210    /**
211    * @return The parsed score values a matrix of bytes
212    */
 
213  2 toggle public byte[][] getScoresArray()
214    {
215  2 if (scores == null)
216    {
217  0 return null;
218    }
219  2 byte[][] result = new byte[scores.size()][];
220   
221  2 int rowCount = 0;
222  2 for (Map.Entry<String, StringBuilder> it : scores.entrySet())
223    {
224  25 String line = it.getValue().toString();
225  25 byte[] seqValues = new byte[line.length()];
226  3284 for (int j = 0, c = line.length(); j < c; j++)
227    {
228   
229  3259 byte val = (byte) (line.charAt(j) - '0');
230   
231  3259 seqValues[j] = (val >= 0 && val <= 9) ? val : -1;
232    }
233   
234  25 result[rowCount++] = seqValues;
235    }
236   
237  2 return result;
238    }
239   
 
240  10 toggle @Override
241    public void parse() throws IOException
242    {
243    /*
244    * read the header
245    */
246  10 header = readHeader(this);
247   
248  10 if (header == null)
249    {
250  3 error = true;
251  3 return;
252    }
253  7 scores = new LinkedHashMap<String, StringBuilder>();
254   
255    /*
256    * initilize the structure
257    */
258  7 for (Map.Entry<String, Integer> entry : header.scores.entrySet())
259    {
260  67 scores.put(entry.getKey(), new StringBuilder());
261    }
262   
263    /*
264    * go with the reading
265    */
266  7 Block block;
267  ? while ((block = readBlock(this, header.scores.size())) != null)
268    {
269   
270    /*
271    * append sequences read in the block
272    */
273  16 for (Map.Entry<String, String> entry : block.items.entrySet())
274    {
275  166 StringBuilder scoreStringBuilder = scores.get(entry.getKey());
276  166 if (scoreStringBuilder == null)
277    {
278  0 error = true;
279  0 errormessage = String.format(
280    "Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
281    entry.getKey());
282  0 return;
283    }
284   
285  166 scoreStringBuilder.append(entry.getValue());
286    }
287    }
288   
289    /*
290    * verify that all rows have the same width
291    */
292  7 for (StringBuilder str : scores.values())
293    {
294  67 if (fWidth == null)
295    {
296  7 fWidth = str.length();
297    }
298  60 else if (fWidth != str.length())
299    {
300  0 error = true;
301  0 errormessage = "Invalid T-Coffee score file: All the score sequences must have the same length";
302  0 return;
303    }
304    }
305   
306  7 return;
307    }
308   
 
309  74 toggle static int parseInt(String str)
310    {
311  74 try
312    {
313  74 return Integer.parseInt(str);
314    } catch (NumberFormatException e)
315    {
316    // TODO report a warning ?
317  0 return 0;
318    }
319    }
320   
321    /**
322    * Reaad the header section in the T-Coffee score file format
323    *
324    * @param reader
325    * The scores reader
326    * @return The parser {@link Header} instance
327    * @throws RuntimeException
328    * when the header is not in the expected format
329    */
 
330  10 toggle static Header readHeader(FileParse reader) throws IOException
331    {
332   
333  10 Header result = null;
334  10 try
335    {
336  10 result = new Header();
337  10 result.head = reader.nextLine();
338   
339  10 String line;
340   
341  ? while ((line = reader.nextLine()) != null)
342    {
343  64 if (line.startsWith("SCORE="))
344    {
345  7 result.score = parseInt(line.substring(6).trim());
346  7 break;
347    }
348    }
349   
350  ? if ((line = reader.nextLine()) == null || !"*".equals(line.trim()))
351    {
352  3 error(reader,
353    "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)");
354  3 return null;
355    }
356  ? if ((line = reader.nextLine()) == null
357    || !"BAD AVG GOOD".equals(line.trim()))
358    {
359  0 error(reader,
360    "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)");
361  0 return null;
362    }
363  ? if ((line = reader.nextLine()) == null || !"*".equals(line.trim()))
364    {
365  0 error(reader,
366    "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)");
367  0 return null;
368    }
369   
370    /*
371    * now are expected a list if sequences ID up to the first blank line
372    */
373  ? while ((line = reader.nextLine()) != null)
374    {
375  74 if ("".equals(line))
376    {
377  7 break;
378    }
379   
380  67 int p = line.indexOf(":");
381  67 if (p == -1)
382    {
383    // TODO report a warning
384  0 continue;
385    }
386   
387  67 String id = line.substring(0, p).trim();
388  67 int val = parseInt(line.substring(p + 1).trim());
389  67 if ("".equals(id))
390    {
391    // TODO report warning
392  0 continue;
393    }
394   
395  67 result.scores.put(id, val);
396    }
397   
398  7 if (result == null)
399    {
400  0 error(reader, "T-COFFEE score file had no per-sequence scores");
401    }
402   
403    } catch (IOException e)
404    {
405  0 error(reader, "Unexpected problem parsing T-Coffee score ascii file");
406  0 throw e;
407    }
408   
409  7 return result;
410    }
411   
 
412  3 toggle private static void error(FileParse reader, String errm)
413    {
414  3 reader.error = true;
415  3 if (reader.errormessage == null)
416    {
417  0 reader.errormessage = errm;
418    }
419    else
420    {
421  3 reader.errormessage += "\n" + errm;
422    }
423    }
424   
425    /**
426    * Read a scores block ihe provided stream.
427    *
428    * @param reader
429    * The stream to parse
430    * @param size
431    * The expected number of the sequence to be read
432    * @return The {@link Block} instance read or {link null} null if the end of
433    * file has reached.
434    * @throws IOException
435    * Something went wrong on the 'wire'
436    */
 
437  24 toggle static Block readBlock(FileParse reader, int size) throws IOException
438    {
439  24 Block result = new Block(size);
440  24 String line;
441   
442    /*
443    * read blank lines (eventually)
444    */
445  ? while ((line = reader.nextLine()) != null && "".equals(line.trim()))
446    {
447    // consume blank lines
448    }
449   
450  24 if (line == null)
451    {
452  7 return null;
453    }
454   
455    /*
456    * read the scores block
457    */
458  17 do
459    {
460  187 if ("".equals(line.trim()))
461    {
462    // terminated
463  12 break;
464    }
465   
466    // split the line on the first blank
467    // the first part have to contain the sequence id
468    // the remaining part are the scores values
469  175 int p = line.indexOf(" ");
470  175 if (p == -1)
471    {
472  0 if (reader.warningMessage == null)
473    {
474  0 reader.warningMessage = "";
475    }
476  0 reader.warningMessage += "Possible parsing error - expected to find a space in line: '"
477    + line + "'\n";
478  0 continue;
479    }
480   
481  175 String id = line.substring(0, p).trim();
482  175 String val = line.substring(p + 1).trim();
483   
484  175 Matcher m = SCORES_WITH_RESIDUE_NUMS.matcher(val);
485  175 if (m.matches())
486    {
487  12 val = m.group(1);
488    }
489   
490  175 result.items.put(id, val);
491   
492  ? } while ((line = reader.nextLine()) != null);
493   
494  17 return result;
495    }
496   
497    /*
498    * The score file header
499    */
 
500    static class Header
501    {
502    String head;
503   
504    int score;
505   
506    LinkedHashMap<String, Integer> scores = new LinkedHashMap<String, Integer>();
507   
 
508  1 toggle public int getScoreAvg()
509    {
510  1 return score;
511    }
512   
 
513  24 toggle public int getScoreFor(String ID)
514    {
515   
516  24 return scores.containsKey(ID) ? scores.get(ID) : -1;
517   
518    }
519    }
520   
521    /*
522    * Hold a single block values block in the score file
523    */
 
524    static class Block
525    {
526    int size;
527   
528    Map<String, String> items;
529   
 
530  24 toggle public Block(int size)
531    {
532  24 this.size = size;
533  24 this.items = new HashMap<String, String>(size);
534    }
535   
 
536  8 toggle String getScoresFor(String id)
537    {
538  8 return items.get(id);
539    }
540   
 
541  1 toggle String getConsensus()
542    {
543  1 return items.get("cons");
544    }
545    }
546   
547    /**
548    * generate annotation for this TCoffee score set on the given alignment
549    *
550    * @param al
551    * alignment to annotate
552    * @param matchids
553    * if true, annotate sequences based on matching sequence names
554    * @return true if alignment annotation was modified, false otherwise.
555    */
 
556  1 toggle public boolean annotateAlignment(AlignmentI al, boolean matchids)
557    {
558  1 if (al.getHeight() != getHeight() || al.getWidth() != getWidth())
559    {
560  0 String info = String.format(
561    "align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(),
562    al.getHeight(), getWidth(), getHeight());
563  0 warningMessage = "Alignment shape does not match T-Coffee score file shape -- "
564    + info;
565  0 return false;
566    }
567  1 boolean added = false;
568  1 int i = 0;
569  1 SequenceIdMatcher sidmatcher = new SequenceIdMatcher(
570    al.getSequencesArray());
571  1 byte[][] scoreMatrix = getScoresArray();
572    // for 2.8 - we locate any existing TCoffee annotation and remove it first
573    // before adding this.
574  1 for (Map.Entry<String, StringBuilder> id : scores.entrySet())
575    {
576  16 byte[] srow = scoreMatrix[i];
577  16 SequenceI s;
578  16 if (matchids)
579    {
580  16 s = sidmatcher.findIdMatch(id.getKey());
581    }
582    else
583    {
584  0 s = al.getSequenceAt(i);
585    }
586  16 i++;
587  16 if (s == null && i != scores.size() && !id.getKey().equals("cons"))
588    {
589  0 System.err
590  0 .println("No " + (matchids ? "match " : " sequences left ")
591    + " for TCoffee score set : " + id.getKey());
592  0 continue;
593    }
594  16 int jSize = al.getWidth() < srow.length ? al.getWidth() : srow.length;
595  16 Annotation[] annotations = new Annotation[al.getWidth()];
596  2528 for (int j = 0; j < jSize; j++)
597    {
598  2512 byte val = srow[j];
599  2512 if (s != null && jalview.util.Comparison.isGap(s.getCharAt(j)))
600    {
601  334 annotations[j] = null;
602  334 if (val > 0)
603    {
604  0 jalview.bin.Console.errPrintln(
605    "Warning: non-zero value for positional T-COFFEE score for gap at "
606    + j + " in sequence " + s.getName());
607    }
608    }
609    else
610    {
611  2178 annotations[j] = new Annotation(s == null ? "" + val : null,
612  2178 s == null ? "" + val : null, '\0', val * 1f,
613  2178 val >= 0 && val < colors.length ? colors[val]
614    : Color.white);
615    }
616    }
617    // this will overwrite any existing t-coffee scores for the alignment
618  16 AlignmentAnnotation aa = al.findOrCreateAnnotation(TCOFFEE_SCORE,
619    TCOFFEE_SCORE, false, s, null);
620  16 if (s != null)
621    {
622  15 aa.label = "T-COFFEE";
623  15 aa.description = "" + id.getKey();
624  15 aa.annotations = annotations;
625  15 aa.visible = false;
626  15 aa.belowAlignment = false;
627  15 aa.setScore(header.getScoreFor(id.getKey()));
628  15 aa.createSequenceMapping(s, s.getStart(), true);
629  15 s.addAlignmentAnnotation(aa);
630  15 aa.adjustForAlignment();
631    }
632    else
633    {
634  1 aa.graph = AlignmentAnnotation.NO_GRAPH;
635  1 aa.label = "T-COFFEE";
636  1 aa.description = "TCoffee column reliability score";
637  1 aa.annotations = annotations;
638  1 aa.belowAlignment = true;
639  1 aa.visible = true;
640  1 aa.setScore(header.getScoreAvg());
641    }
642  16 aa.showAllColLabels = true;
643  16 aa.validateRangeAndDisplay();
644  16 added = true;
645    }
646   
647  1 return added;
648    }
649   
 
650  0 toggle @Override
651    public String print(SequenceI[] sqs, boolean jvsuffix)
652    {
653    // TODO Auto-generated method stub
654  0 return "Not valid.";
655    }
656    }
  • Report generated by OpenClover v 4.4.1 on Fri Dec 6 2024 13:54:25 GMT using coverage data from Fri Dec 6 2024 13:54:13 GMT.
  • OpenClover is free and open-source software.