Clover icon

Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.io

File SequenceAnnotationReport.java

 

Coverage histogram

../../img/srcFileCovDistChart9.png
12% of files have more coverage

Code metrics

110
184
13
1
616
407
85
0.46
14.15
13
6.54

Classes

Class Line # Actions
SequenceAnnotationReport 46 184 85
0.811074981.1%
 

Contributing tests

This file is covered by 106 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 java.util.Collection;
24    import java.util.Comparator;
25    import java.util.LinkedHashMap;
26    import java.util.List;
27    import java.util.Map;
28   
29    import jalview.api.FeatureColourI;
30    import jalview.datamodel.DBRefEntry;
31    import jalview.datamodel.DBRefSource;
32    import jalview.datamodel.GeneLociI;
33    import jalview.datamodel.MappedFeatures;
34    import jalview.datamodel.SequenceFeature;
35    import jalview.datamodel.SequenceI;
36    import jalview.util.MessageManager;
37    import jalview.util.StringUtils;
38    import jalview.util.UrlLink;
39    import jalview.viewmodel.seqfeatures.FeatureRendererModel;
40   
41    /**
42    * generate HTML reports for a sequence
43    *
44    * @author jimp
45    */
 
46    public class SequenceAnnotationReport
47    {
48    private static final int MAX_DESCRIPTION_LENGTH = 40;
49   
50    private static final String COMMA = ",";
51   
52    private static final String ELLIPSIS = "...";
53   
54    private static final int MAX_REFS_PER_SOURCE = 4;
55   
56    private static final int MAX_SOURCES = 40;
57   
58    private static String linkImageURL;
59   
60    // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
61   
62    /*
63    * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
64    * with 'Primary' sources placed before others, and 'chromosome' first of all
65    */
66    private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
67    {
68   
 
69  145 toggle @Override
70    public int compare(DBRefEntry ref1, DBRefEntry ref2)
71    {
72  145 if (ref1 instanceof GeneLociI)
73    {
74  0 return -1;
75    }
76  145 if (ref2 instanceof GeneLociI)
77    {
78  0 return 1;
79    }
80  145 String s1 = ref1.getSource();
81  145 String s2 = ref2.getSource();
82  145 boolean s1Primary = DBRefSource.isPrimarySource(s1);
83  145 boolean s2Primary = DBRefSource.isPrimarySource(s2);
84  145 if (s1Primary && !s2Primary)
85    {
86  26 return -1;
87    }
88  119 if (!s1Primary && s2Primary)
89    {
90  1 return 1;
91    }
92  118 int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
93    .compareToIgnoreCase(s2));
94  118 if (comp == 0)
95    {
96  5 String a1 = ref1.getAccessionId();
97  5 String a2 = ref2.getAccessionId();
98  5 comp = a1 == null ? -1 : (a2 == null ? 1 : a1
99    .compareToIgnoreCase(a2));
100    }
101  118 return comp;
102    }
103   
104    // private boolean isPrimarySource(String source)
105    // {
106    // for (String[] primary : DBRefSource.PRIMARY_SOURCES)
107    // {
108    // for (String s : primary)
109    // {
110    // if (source.equals(s))
111    // {
112    // return true;
113    // }
114    // }
115    // }
116    // return false;
117    // }
118    };
119   
120    private boolean forTooltip;
121   
122    /**
123    * Constructor given a flag which affects behaviour
124    * <ul>
125    * <li>if true, generates feature details suitable to show in a tooltip</li>
126    * <li>if false, generates feature details in a form suitable for the sequence
127    * details report</li>
128    * </ul>
129    *
130    * @param isForTooltip
131    */
 
132  546 toggle public SequenceAnnotationReport(boolean isForTooltip)
133    {
134  546 this.forTooltip = isForTooltip;
135  546 if (linkImageURL == null)
136    {
137  18 linkImageURL = getClass().getResource("/images/link.gif").toString();
138    }
139    }
140   
141    /**
142    * Append text for the list of features to the tooltip. Returns the number of
143    * features not added if maxlength limit is (or would have been) reached.
144    *
145    * @param sb
146    * @param residuePos
147    * @param features
148    * @param minmax
149    * @param maxlength
150    */
 
151  1 toggle public int appendFeatures(final StringBuilder sb,
152    int residuePos, List<SequenceFeature> features,
153    FeatureRendererModel fr, int maxlength)
154    {
155  4 for (int i = 0; i < features.size(); i++)
156    {
157  4 SequenceFeature feature = features.get(i);
158  4 if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
159    {
160  1 return features.size() - i;
161    }
162    }
163  0 return 0;
164    }
165   
166    /**
167    * Appends text for mapped features (e.g. CDS feature for peptide or vice
168    * versa) Returns number of features left if maxlength limit is (or would have
169    * been) reached.
170    *
171    * @param sb
172    * @param residuePos
173    * @param mf
174    * @param fr
175    * @param maxlength
176    */
 
177  0 toggle public int appendFeatures(StringBuilder sb, int residuePos,
178    MappedFeatures mf, FeatureRendererModel fr, int maxlength)
179    {
180  0 for (int i = 0; i < mf.features.size(); i++)
181    {
182  0 SequenceFeature feature = mf.features.get(i);
183  0 if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
184    {
185  0 return mf.features.size() - i;
186    }
187    }
188  0 return 0;
189    }
190   
191    /**
192    * Appends the feature at rpos to the given buffer
193    *
194    * @param sb
195    * @param rpos
196    * @param minmax
197    * @param feature
198    */
 
199  41 toggle boolean appendFeature(final StringBuilder sb0, int rpos,
200    FeatureRendererModel fr, SequenceFeature feature,
201    MappedFeatures mf, int maxlength)
202    {
203  41 int begin = feature.getBegin();
204  41 int end = feature.getEnd();
205   
206    /*
207    * if this is a virtual features, convert begin/end to the
208    * coordinates of the sequence it is mapped to
209    */
210  41 int[] beginRange = null;
211  41 int[] endRange = null;
212  41 if (mf != null)
213    {
214  3 beginRange = mf.getMappedPositions(begin, begin);
215  3 endRange = mf.getMappedPositions(end, end);
216  3 if (beginRange == null || endRange == null)
217    {
218    // something went wrong
219  0 return false;
220    }
221  3 begin = beginRange[0];
222  3 end = endRange[endRange.length - 1];
223    }
224   
225  41 StringBuilder sb = new StringBuilder();
226  41 if (feature.isContactFeature())
227    {
228    /*
229    * include if rpos is at start or end position of [mapped] feature
230    */
231  3 boolean showContact = (mf == null) && (rpos == begin || rpos == end);
232  3 boolean showMappedContact = (mf != null) && ((rpos >= beginRange[0]
233    && rpos <= beginRange[beginRange.length - 1])
234    || (rpos >= endRange[0]
235    && rpos <= endRange[endRange.length - 1]));
236  3 if (showContact || showMappedContact)
237    {
238  2 if (sb0.length() > 6)
239    {
240  1 sb.append("<br/>");
241    }
242  2 sb.append(feature.getType()).append(" ").append(begin).append(":")
243    .append(end);
244    }
245  3 return appendText(sb0, sb, maxlength);
246    }
247   
248  38 if (sb0.length() > 6)
249    {
250  21 sb.append("<br/>");
251    }
252    // TODO: remove this hack to display link only features
253  38 boolean linkOnly = feature.getValue("linkonly") != null;
254  38 if (!linkOnly)
255    {
256  38 sb.append(feature.getType()).append(" ");
257  38 if (rpos != 0)
258    {
259    // we are marking a positional feature
260  21 sb.append(begin);
261  21 if (begin != end)
262    {
263  19 sb.append(" ").append(end);
264    }
265    }
266   
267  38 String description = feature.getDescription();
268  38 if (description != null && !description.equals(feature.getType()))
269    {
270  37 description = StringUtils.stripHtmlTags(description);
271   
272    /*
273    * truncate overlong descriptions unless they contain an href
274    * before the truncation point (as truncation could leave corrupted html)
275    */
276  37 int linkindex = description.toLowerCase().indexOf("<a ");
277  37 boolean hasLink = linkindex > -1
278    && linkindex < MAX_DESCRIPTION_LENGTH;
279  37 if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
280    {
281  6 description = description.substring(0, MAX_DESCRIPTION_LENGTH)
282    + ELLIPSIS;
283    }
284   
285  37 sb.append("; ").append(description);
286    }
287   
288  38 if (showScore(feature, fr))
289    {
290  5 sb.append(" Score=").append(String.valueOf(feature.getScore()));
291    }
292  38 String status = (String) feature.getValue("status");
293  38 if (status != null && status.length() > 0)
294    {
295  2 sb.append("; (").append(status).append(")");
296    }
297   
298    /*
299    * add attribute value if coloured by attribute
300    */
301  38 if (fr != null)
302    {
303  27 FeatureColourI fc = fr.getFeatureColours().get(feature.getType());
304  27 if (fc != null && fc.isColourByAttribute())
305    {
306  5 String[] attName = fc.getAttributeName();
307  5 String attVal = feature.getValueAsString(attName);
308  5 if (attVal != null)
309    {
310  4 sb.append("; ").append(String.join(":", attName)).append("=")
311    .append(attVal);
312    }
313    }
314    }
315   
316  38 if (mf != null)
317    {
318  3 String variants = mf.findProteinVariants(feature);
319  3 if (!variants.isEmpty())
320    {
321  1 sb.append(" ").append(variants);
322    }
323    }
324    }
325  38 return appendText(sb0, sb, maxlength);
326    }
327   
328    /**
329    * Appends sb to sb0, and returns false, unless maxlength is not zero and
330    * appending would make the result longer than or equal to maxlength, in which
331    * case the append is not done and returns true
332    *
333    * @param sb0
334    * @param sb
335    * @param maxlength
336    * @return
337    */
 
338  41 toggle private static boolean appendText(StringBuilder sb0, StringBuilder sb,
339    int maxlength)
340    {
341  41 if (maxlength == 0 || sb0.length() + sb.length() < maxlength)
342    {
343  40 sb0.append(sb);
344  40 return false;
345    }
346  1 return true;
347    }
348   
349    /**
350    * Answers true if score should be shown, else false. Score is shown if it is
351    * not NaN, and the feature type has a non-trivial min-max score range
352    */
 
353  38 toggle boolean showScore(SequenceFeature feature, FeatureRendererModel fr)
354    {
355  38 if (Float.isNaN(feature.getScore()))
356    {
357  11 return false;
358    }
359  27 if (fr == null)
360    {
361  3 return true;
362    }
363  24 float[][] minMax = fr.getMinMax().get(feature.getType());
364   
365    /*
366    * minMax[0] is the [min, max] score range for positional features
367    */
368  24 if (minMax == null || minMax[0] == null || minMax[0][0] == minMax[0][1])
369    {
370  22 return false;
371    }
372  2 return true;
373    }
374   
375    /**
376    * Format and appends any hyperlinks for the sequence feature to the string
377    * buffer
378    *
379    * @param sb
380    * @param feature
381    */
 
382  0 toggle void appendLinks(final StringBuffer sb, SequenceFeature feature)
383    {
384  0 if (feature.links != null)
385    {
386  0 if (linkImageURL != null)
387    {
388  0 sb.append(" <img src=\"" + linkImageURL + "\">");
389    }
390    else
391    {
392  0 for (String urlstring : feature.links)
393    {
394  0 try
395    {
396  0 for (List<String> urllink : createLinksFrom(null, urlstring))
397    {
398  0 sb.append("<br/> <a href=\""
399    + urllink.get(3)
400    + "\" target=\""
401    + urllink.get(0)
402    + "\">"
403  0 + (urllink.get(0).toLowerCase()
404    .equals(urllink.get(1).toLowerCase()) ? urllink
405    .get(0) : (urllink.get(0) + ":" + urllink
406    .get(1)))
407    + "</a><br/>");
408    }
409    } catch (Exception x)
410    {
411  0 System.err.println("problem when creating links from "
412    + urlstring);
413  0 x.printStackTrace();
414    }
415    }
416    }
417   
418    }
419    }
420   
421    /**
422    *
423    * @param seq
424    * @param link
425    * @return Collection< List<String> > { List<String> { link target, link
426    * label, dynamic component inserted (if any), url }}
427    */
 
428  0 toggle Collection<List<String>> createLinksFrom(SequenceI seq, String link)
429    {
430  0 Map<String, List<String>> urlSets = new LinkedHashMap<>();
431  0 UrlLink urlLink = new UrlLink(link);
432  0 if (!urlLink.isValid())
433    {
434  0 System.err.println(urlLink.getInvalidMessage());
435  0 return null;
436    }
437   
438  0 urlLink.createLinksFromSeq(seq, urlSets);
439   
440  0 return urlSets.values();
441    }
442   
 
443  10 toggle public void createSequenceAnnotationReport(final StringBuilder tip,
444    SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
445    FeatureRendererModel fr)
446    {
447  10 createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
448    fr, false);
449    }
450   
451    /**
452    * Builds an html formatted report of sequence details and appends it to the
453    * provided buffer.
454    *
455    * @param sb
456    * buffer to append report to
457    * @param sequence
458    * the sequence the report is for
459    * @param showDbRefs
460    * whether to include database references for the sequence
461    * @param showNpFeats
462    * whether to include non-positional sequence features
463    * @param fr
464    * @param summary
465    * @return
466    */
 
467  11 toggle int createSequenceAnnotationReport(final StringBuilder sb,
468    SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
469    FeatureRendererModel fr, boolean summary)
470    {
471  11 String tmp;
472  11 sb.append("<i>");
473   
474  11 int maxWidth = 0;
475  11 if (sequence.getDescription() != null)
476    {
477  10 tmp = sequence.getDescription();
478  10 sb.append(tmp);
479  10 maxWidth = Math.max(maxWidth, tmp.length());
480    }
481  11 SequenceI ds = sequence;
482  11 while (ds.getDatasetSequence() != null)
483    {
484  0 ds = ds.getDatasetSequence();
485    }
486   
487  11 if (showDbRefs)
488    {
489  9 maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
490    }
491   
492    /*
493    * add non-positional features if wanted
494    */
495  11 if (showNpFeats)
496    {
497  9 for (SequenceFeature sf : sequence.getFeatures()
498    .getNonPositionalFeatures())
499    {
500  17 int sz = -sb.length();
501  17 appendFeature(sb, 0, fr, sf, null, 0);
502  17 sz += sb.length();
503  17 maxWidth = Math.max(maxWidth, sz);
504    }
505    }
506  11 sb.append("</i>");
507  11 return maxWidth;
508    }
509   
510    /**
511    * A helper method that appends any DBRefs, returning the maximum line length
512    * added
513    *
514    * @param sb
515    * @param ds
516    * @param summary
517    * @return
518    */
 
519  9 toggle protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
520    boolean summary)
521    {
522  9 List<DBRefEntry> dbrefs = ds.getDBRefs();
523  9 if (dbrefs == null)
524    {
525  6 return 0;
526    }
527   
528    // note this sorts the refs held on the sequence!
529  3 dbrefs.sort(comparator);
530  3 boolean ellipsis = false;
531  3 String source = null;
532  3 String lastSource = null;
533  3 int countForSource = 0;
534  3 int sourceCount = 0;
535  3 boolean moreSources = false;
536  3 int maxLineLength = 0;
537  3 int lineLength = 0;
538   
539  3 for (DBRefEntry ref : dbrefs)
540    {
541  49 source = ref.getSource();
542  49 if (source == null)
543    {
544    // shouldn't happen
545  0 continue;
546    }
547  49 boolean sourceChanged = !source.equals(lastSource);
548  49 if (sourceChanged)
549    {
550  45 lineLength = 0;
551  45 countForSource = 0;
552  45 sourceCount++;
553    }
554  49 if (sourceCount > MAX_SOURCES && summary)
555    {
556  1 ellipsis = true;
557  1 moreSources = true;
558  1 break;
559    }
560  48 lastSource = source;
561  48 countForSource++;
562  48 if (countForSource == 1 || !summary)
563    {
564  44 sb.append("<br/>");
565    }
566  48 if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
567    {
568  47 String accessionId = ref.getAccessionId();
569  47 lineLength += accessionId.length() + 1;
570  47 if (countForSource > 1 && summary)
571    {
572  3 sb.append(", ").append(accessionId);
573  3 lineLength++;
574    }
575    else
576    {
577  44 sb.append(source).append(" ").append(accessionId);
578  44 lineLength += source.length();
579    }
580  47 maxLineLength = Math.max(maxLineLength, lineLength);
581    }
582  48 if (countForSource == MAX_REFS_PER_SOURCE && summary)
583    {
584  1 sb.append(COMMA).append(ELLIPSIS);
585  1 ellipsis = true;
586    }
587    }
588  3 if (moreSources)
589    {
590  1 sb.append("<br/>").append(source).append(COMMA).append(ELLIPSIS);
591    }
592  3 if (ellipsis)
593    {
594  1 sb.append("<br/>(");
595  1 sb.append(MessageManager.getString("label.output_seq_details"));
596  1 sb.append(")");
597    }
598   
599  3 return maxLineLength;
600    }
601   
 
602  0 toggle public void createTooltipAnnotationReport(final StringBuilder tip,
603    SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
604    FeatureRendererModel fr)
605    {
606  0 int maxWidth = createSequenceAnnotationReport(tip, sequence,
607    showDbRefs, showNpFeats, fr, true);
608   
609  0 if (maxWidth > 60)
610    {
611    // ? not sure this serves any useful purpose
612    // tip.insert(0, "<table width=350 border=0><tr><td>");
613    // tip.append("</td></tr></table>");
614    }
615    }
616    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.