Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceAnnotationReport	48	195	91	0.00%	Show methods

Class SequenceAnnotationReport

Class SequenceAnnotationReport	Line # 48	Total Statements 195	Complexity 91	TOTAL Coverage 0.00%
compare(DBRefEntry,DBRefEntry) : int   compare(DBRefEntry,DBRefEntry) : int	7171	22.022	16.016	0.0 0.00%
SequenceAnnotationReport(boolean)   SequenceAnnotationReport(boolean)	143143	3.03	2.02	0.0 0.00%
appendFeatures(StringBuilder,int,List<SequenceFeature>,FeatureRendererModel,int) : int   appendFeatures(StringBuilder,int,List<SequenceFeature>,FeatureRendererModel,int) : int	162162	5.05	3.03	0.0 0.00%
appendFeatures(StringBuilder,int,MappedFeatures,FeatureRendererModel,int) : int   appendFeatures(StringBuilder,int,MappedFeatures,FeatureRendererModel,int) : int	188188	5.05	3.03	0.0 0.00%
appendFeature(StringBuilder,int,FeatureRendererModel,SequenceFeature,MappedFeatures,int) : boolean   appendFeature(StringBuilder,int,FeatureRendererModel,SequenceFeature,MappedFeatures,int) : boolean	210210	57.057	27.027	0.0 0.00%
appendText(StringBuilder,StringBuilder,int) : boolean   appendText(StringBuilder,StringBuilder,int) : boolean	364364	4.04	3.03	0.0 0.00%
showScore(SequenceFeature,FeatureRendererModel) : boolean   showScore(SequenceFeature,FeatureRendererModel) : boolean	379379	8.08	6.06	0.0 0.00%
appendLinks(StringBuffer,SequenceFeature) : void   appendLinks(StringBuffer,SequenceFeature) : void	408408	9.09	5.05	0.0 0.00%
createLinksFrom(SequenceI,String) : Collection<List<String>>   createLinksFrom(SequenceI,String) : Collection<List<String>>	452452	7.07	2.02	0.0 0.00%
createSequenceAnnotationReport(StringBuilder,SequenceI,boolean,boolean,FeatureRendererModel) : void   createSequenceAnnotationReport(StringBuilder,SequenceI,boolean,boolean,FeatureRendererModel) : void	467467	1.01	1.01	0.0 0.00%
createSequenceAnnotationReport(StringBuilder,SequenceI,boolean,boolean,FeatureRendererModel,boolean) : int   createSequenceAnnotationReport(StringBuilder,SequenceI,boolean,boolean,FeatureRendererModel,boolean) : int	491491	22.022	5.05	0.0 0.00%
appendDbRefs(StringBuilder,SequenceI,boolean) : int   appendDbRefs(StringBuilder,SequenceI,boolean) : int	545545	50.050	16.016	0.0 0.00%
createTooltipAnnotationReport(StringBuilder,SequenceI,boolean,boolean,FeatureRendererModel) : void   createTooltipAnnotationReport(StringBuilder,SequenceI,boolean,boolean,FeatureRendererModel) : void	635635	2.02	2.02	0.0 0.00%

 

Contributing tests

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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.ArrayList;
24		import java.util.Collection;
25		import java.util.Comparator;
26		import java.util.LinkedHashMap;
27		import java.util.List;
28		import java.util.Locale;
29		import java.util.Map;
30
31		import jalview.api.FeatureColourI;
32		import jalview.datamodel.DBRefEntry;
33		import jalview.datamodel.DBRefSource;
34		import jalview.datamodel.GeneLociI;
35		import jalview.datamodel.MappedFeatures;
36		import jalview.datamodel.SequenceFeature;
37		import jalview.datamodel.SequenceI;
38		import jalview.util.MessageManager;
39		import jalview.util.StringUtils;
40		import jalview.util.UrlLink;
41		import jalview.viewmodel.seqfeatures.FeatureRendererModel;
42
43		/**
44		* generate HTML reports for a sequence
45		*
46		* @author jimp
47		*/
		0% Uncovered Elements: 326 (326) Complexity: 91 Complexity Density: 0.47
48		public class SequenceAnnotationReport
49		{
50		private static final int MAX_DESCRIPTION_LENGTH = 40;
51
52		private static final String COMMA = ",";
53
54		private static final String ELLIPSIS = "...";
55
56		private static final int MAX_REFS_PER_SOURCE = 4;
57
58		private static final int MAX_SOURCES = 5;
59
60		private static String linkImageURL;
61
62		// public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
63
64		/*
65		* Comparator to order DBRefEntry by Source + accession id (case-insensitive),
66		* with 'Primary' sources placed before others, and 'chromosome' first of all
67		*/
68		private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
69		{
70
		0% Uncovered Elements: 44 (44) Complexity: 16 Complexity Density: 0.73
71	0	@Override...
72		public int compare(DBRefEntry ref1, DBRefEntry ref2)
73		{
74	0	if (ref1 instanceof GeneLociI)
75		{
76	0	return -1;
77		}
78	0	if (ref2 instanceof GeneLociI)
79		{
80	0	return 1;
81		}
82
83	0	String s1 = ref1.getSource();
84	0	String s2 = ref2.getSource();
85	0	boolean s1Primary = DBRefSource.isPrimarySource(s1);
86	0	boolean s2Primary = DBRefSource.isPrimarySource(s2);
87	0	if (ref1.isCanonical() && !ref2.isCanonical())
88		{
89	0	return -1;
90		}
91	0	if (!ref1.isCanonical() && ref2.isCanonical())
92		{
93	0	return 1;
94		}
95	0	if (s1Primary && !s2Primary)
96		{
97	0	return -1;
98		}
99	0	if (!s1Primary && s2Primary)
100		{
101	0	return 1;
102		}
103	0	int comp = s1 == null ? -1
104	0	: (s2 == null ? 1 : s1.compareToIgnoreCase(s2));
105	0	if (comp == 0)
106		{
107	0	String a1 = ref1.getAccessionId();
108	0	String a2 = ref2.getAccessionId();
109	0	comp = a1 == null ? -1
110	0	: (a2 == null ? 1 : a1.compareToIgnoreCase(a2));
111		}
112	0	return comp;
113		}
114
115		// private boolean isPrimarySource(String source)
116		// {
117		// for (String[] primary : DBRefSource.PRIMARY_SOURCES)
118		// {
119		// for (String s : primary)
120		// {
121		// if (source.equals(s))
122		// {
123		// return true;
124		// }
125		// }
126		// }
127		// return false;
128		// }
129		};
130
131		private boolean forTooltip;
132
133		/**
134		* Constructor given a flag which affects behaviour
135		* <ul>
136		* <li>if true, generates feature details suitable to show in a tooltip</li>
137		* <li>if false, generates feature details in a form suitable for the sequence
138		* details report</li>
139		* </ul>
140		*
141		* @param isForTooltip
142		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
143	0	public SequenceAnnotationReport(boolean isForTooltip)...
144		{
145	0	this.forTooltip = isForTooltip;
146	0	if (linkImageURL == null)
147		{
148	0	linkImageURL = getClass().getResource("/images/link.gif").toString();
149		}
150		}
151
152		/**
153		* Append text for the list of features to the tooltip. Returns the number of
154		* features not added if maxlength limit is (or would have been) reached.
155		*
156		* @param sb
157		* @param residuePos
158		* @param features
159		* @param minmax
160		* @param maxlength
161		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
162	0	public int appendFeatures(final StringBuilder sb, int residuePos,...
163		List<SequenceFeature> features, FeatureRendererModel fr,
164		int maxlength)
165		{
166	0	for (int i = 0; i < features.size(); i++)
167		{
168	0	SequenceFeature feature = features.get(i);
169	0	if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
170		{
171	0	return features.size() - i;
172		}
173		}
174	0	return 0;
175		}
176
177		/**
178		* Appends text for mapped features (e.g. CDS feature for peptide or vice
179		* versa) Returns number of features left if maxlength limit is (or would have
180		* been) reached.
181		*
182		* @param sb
183		* @param residuePos
184		* @param mf
185		* @param fr
186		* @param maxlength
187		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
188	0	public int appendFeatures(StringBuilder sb, int residuePos,...
189		MappedFeatures mf, FeatureRendererModel fr, int maxlength)
190		{
191	0	for (int i = 0; i < mf.features.size(); i++)
192		{
193	0	SequenceFeature feature = mf.features.get(i);
194	0	if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
195		{
196	0	return mf.features.size() - i;
197		}
198		}
199	0	return 0;
200		}
201
202		/**
203		* Appends the feature at rpos to the given buffer
204		*
205		* @param sb
206		* @param rpos
207		* @param minmax
208		* @param feature
209		*/
		0% Uncovered Elements: 97 (97) Complexity: 27 Complexity Density: 0.47
210	0	boolean appendFeature(final StringBuilder sb0, int rpos,...
211		FeatureRendererModel fr, SequenceFeature feature,
212		MappedFeatures mf, int maxlength)
213		{
214	0	int begin = feature.getBegin();
215	0	int end = feature.getEnd();
216
217		/*
218		* if this is a virtual features, convert begin/end to the
219		* coordinates of the sequence it is mapped to
220		*/
221	0	int[] beginRange = null; // feature start in local coordinates
222	0	int[] endRange = null; // feature end in local coordinates
223	0	if (mf != null)
224		{
225	0	if (feature.isContactFeature())
226		{
227		/*
228		* map start and end points individually
229		*/
230	0	beginRange = mf.getMappedPositions(begin, begin);
231	0	endRange = begin == end ? beginRange
232		: mf.getMappedPositions(end, end);
233		}
234		else
235		{
236		/*
237		* map the feature extent
238		*/
239	0	beginRange = mf.getMappedPositions(begin, end);
240	0	endRange = beginRange;
241		}
242	0	if (beginRange == null || endRange == null)
243		{
244		// something went wrong
245	0	return false;
246		}
247	0	begin = beginRange[0];
248	0	end = endRange[endRange.length - 1];
249		}
250
251	0	StringBuilder sb = new StringBuilder();
252	0	if (feature.isContactFeature())
253		{
254		/*
255		* include if rpos is at start or end position of [mapped] feature
256		*/
257	0	boolean showContact = (mf == null) && (rpos == begin || rpos == end);
258	0	boolean showMappedContact = (mf != null) && ((rpos >= beginRange[0]
259		&& rpos <= beginRange[beginRange.length - 1])
260		|| (rpos >= endRange[0]
261		&& rpos <= endRange[endRange.length - 1]));
262	0	if (showContact || showMappedContact)
263		{
264	0	if (sb0.length() > 6)
265		{
266	0	sb.append("<br/>");
267		}
268	0	sb.append(feature.getType()).append(" ").append(begin).append(":")
269		.append(end);
270		}
271	0	return appendText(sb0, sb, maxlength);
272		}
273
274	0	if (sb0.length() > 6)
275		{
276	0	sb.append("<br/>");
277		}
278		// TODO: remove this hack to display link only features
279	0	boolean linkOnly = feature.getValue("linkonly") != null;
280	0	if (!linkOnly)
281		{
282	0	sb.append(feature.getType()).append(" ");
283	0	if (rpos != 0)
284		{
285		// we are marking a positional feature
286	0	sb.append(begin);
287	0	if (begin != end)
288		{
289	0	sb.append(" ").append(end);
290		}
291		}
292
293	0	String description = feature.getDescription();
294	0	if (description != null && !description.equals(feature.getType()))
295		{
296	0	description = StringUtils.stripHtmlTags(description);
297
298		/*
299		* truncate overlong descriptions unless they contain an href
300		* before the truncation point (as truncation could leave corrupted html)
301		*/
302	0	int linkindex = description.toLowerCase(Locale.ROOT).indexOf("<a ");
303	0	boolean hasLink = linkindex > -1
304		&& linkindex < MAX_DESCRIPTION_LENGTH;
305	0	if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
306		{
307	0	description = description.substring(0, MAX_DESCRIPTION_LENGTH)
308		+ ELLIPSIS;
309		}
310
311	0	sb.append("; ").append(description);
312		}
313
314	0	if (showScore(feature, fr))
315		{
316	0	sb.append(" Score=").append(String.valueOf(feature.getScore()));
317		}
318	0	String status = (String) feature.getValue("status");
319	0	if (status != null && status.length() > 0)
320		{
321	0	sb.append("; (").append(status).append(")");
322		}
323
324		/*
325		* add attribute value if coloured by attribute
326		*/
327	0	if (fr != null)
328		{
329	0	FeatureColourI fc = fr.getFeatureColours().get(feature.getType());
330	0	if (fc != null && fc.isColourByAttribute())
331		{
332	0	String[] attName = fc.getAttributeName();
333	0	String attVal = feature.getValueAsString(attName);
334	0	if (attVal != null)
335		{
336	0	sb.append("; ").append(String.join(":", attName)).append("=")
337		.append(attVal);
338		}
339		}
340		}
341
342	0	if (mf != null)
343		{
344	0	String variants = mf.findProteinVariants(feature);
345	0	if (!variants.isEmpty())
346		{
347	0	sb.append(" ").append(variants);
348		}
349		}
350		}
351	0	return appendText(sb0, sb, maxlength);
352		}
353
354		/**
355		* Appends sb to sb0, and returns false, unless maxlength is not zero and
356		* appending would make the result longer than or equal to maxlength, in which
357		* case the append is not done and returns true
358		*
359		* @param sb0
360		* @param sb
361		* @param maxlength
362		* @return
363		*/
		0% Uncovered Elements: 6 (6) Complexity: 3 Complexity Density: 0.75
364	0	private static boolean appendText(StringBuilder sb0, StringBuilder sb,...
365		int maxlength)
366		{
367	0	if (maxlength == 0 || sb0.length() + sb.length() < maxlength)
368		{
369	0	sb0.append(sb);
370	0	return false;
371		}
372	0	return true;
373		}
374
375		/**
376		* Answers true if score should be shown, else false. Score is shown if it is
377		* not NaN, and the feature type has a non-trivial min-max score range
378		*/
		0% Uncovered Elements: 14 (14) Complexity: 6 Complexity Density: 0.75
379	0	boolean showScore(SequenceFeature feature, FeatureRendererModel fr)...
380		{
381	0	if (Float.isNaN(feature.getScore()))
382		{
383	0	return false;
384		}
385	0	if (fr == null)
386		{
387	0	return true;
388		}
389	0	float[][] minMax = fr.getMinMax().get(feature.getType());
390
391		/*
392		* minMax[0] is the [min, max] score range for positional features
393		*/
394	0	if (minMax == null || minMax[0] == null || minMax[0][0] == minMax[0][1])
395		{
396	0	return false;
397		}
398	0	return true;
399		}
400
401		/**
402		* Format and appends any hyperlinks for the sequence feature to the string
403		* buffer
404		*
405		* @param sb
406		* @param feature
407		*/
		0% Uncovered Elements: 15 (15) Complexity: 5 Complexity Density: 0.56
408	0	void appendLinks(final StringBuffer sb, SequenceFeature feature)...
409		{
410	0	if (feature.links != null)
411		{
412	0	if (linkImageURL != null)
413		{
414	0	sb.append(" <img src=\"" + linkImageURL + "\">");
415		}
416		else
417		{
418	0	for (String urlstring : feature.links)
419		{
420	0	try
421		{
422	0	for (List<String> urllink : createLinksFrom(null, urlstring))
423		{
424	0	sb.append("<br/> <a href=\"" + urllink.get(3) + "\" target=\""
425		+ urllink.get(0) + "\">"
426	0	+ (urllink.get(0).toLowerCase(Locale.ROOT).equals(
427		urllink.get(1).toLowerCase(Locale.ROOT))
428		? urllink.get(0)
429		: (urllink.get(0) + ":"
430		+ urllink.get(1)))
431		+ "</a><br/>");
432		}
433		} catch (Exception x)
434		{
435	0	jalview.bin.Console.errPrintln(
436		"problem when creating links from " + urlstring);
437	0	x.printStackTrace();
438		}
439		}
440		}
441
442		}
443		}
444
445		/**
446		*
447		* @param seq
448		* @param link
449		* @return Collection< List<String> > { List<String> { link target, link
450		* label, dynamic component inserted (if any), url }}
451		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
452	0	Collection<List<String>> createLinksFrom(SequenceI seq, String link)...
453		{
454	0	Map<String, List<String>> urlSets = new LinkedHashMap<>();
455	0	UrlLink urlLink = new UrlLink(link);
456	0	if (!urlLink.isValid())
457		{
458	0	jalview.bin.Console.errPrintln(urlLink.getInvalidMessage());
459	0	return null;
460		}
461
462	0	urlLink.createLinksFromSeq(seq, urlSets);
463
464	0	return urlSets.values();
465		}
466
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
467	0	public void createSequenceAnnotationReport(final StringBuilder tip,...
468		SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
469		FeatureRendererModel fr)
470		{
471	0	createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
472		fr, false);
473		}
474
475		/**
476		* Builds an html formatted report of sequence details and appends it to the
477		* provided buffer.
478		*
479		* @param sb
480		* buffer to append report to
481		* @param sequence
482		* the sequence the report is for
483		* @param showDbRefs
484		* whether to include database references for the sequence
485		* @param showNpFeats
486		* whether to include non-positional sequence features
487		* @param fr
488		* @param summary
489		* @return
490		*/
		0% Uncovered Elements: 30 (30) Complexity: 5 Complexity Density: 0.23
491	0	int createSequenceAnnotationReport(final StringBuilder sb,...
492		SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
493		FeatureRendererModel fr, boolean summary)
494		{
495	0	String tmp;
496	0	sb.append("<i>");
497
498	0	int maxWidth = 0;
499	0	if (sequence.getDescription() != null)
500		{
501	0	tmp = sequence.getDescription();
502	0	sb.append(tmp);
503	0	maxWidth = Math.max(maxWidth, tmp.length());
504		}
505	0	sb.append("\n");
506	0	SequenceI ds = sequence;
507	0	while (ds.getDatasetSequence() != null)
508		{
509	0	ds = ds.getDatasetSequence();
510		}
511
512	0	if (showDbRefs)
513		{
514	0	maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
515		}
516	0	sb.append("\n");
517
518		/*
519		* add non-positional features if wanted
520		*/
521	0	if (showNpFeats)
522		{
523	0	for (SequenceFeature sf : sequence.getFeatures()
524		.getNonPositionalFeatures())
525		{
526	0	int sz = -sb.length();
527	0	appendFeature(sb, 0, fr, sf, null, 0);
528	0	sz += sb.length();
529	0	maxWidth = Math.max(maxWidth, sz);
530		}
531		}
532	0	sb.append("</i>");
533	0	return maxWidth;
534		}
535
536		/**
537		* A helper method that appends any DBRefs, returning the maximum line length
538		* added
539		*
540		* @param sb
541		* @param ds
542		* @param summary
543		* @return
544		*/
		0% Uncovered Elements: 70 (70) Complexity: 16 Complexity Density: 0.32
545	0	protected int appendDbRefs(final StringBuilder sb, SequenceI ds,...
546		boolean summary)
547		{
548	0	List<DBRefEntry> dbrefs, dbrefset = ds.getDBRefs();
549
550	0	if (dbrefset == null)
551		{
552	0	return 0;
553		}
554
555		// PATCH for JAL-3980 defensive copy
556
557	0	dbrefs = new ArrayList<DBRefEntry>();
558
559	0	dbrefs.addAll(dbrefset);
560
561		// note this sorts the refs held on the sequence!
562	0	dbrefs.sort(comparator);
563	0	boolean ellipsis = false;
564	0	String source = null;
565	0	String lastSource = null;
566	0	int countForSource = 0;
567	0	int sourceCount = 0;
568	0	boolean moreSources = false;
569	0	int maxLineLength = 0;
570	0	int lineLength = 0;
571
572	0	for (DBRefEntry ref : dbrefs)
573		{
574	0	source = ref.getSource();
575	0	if (source == null)
576		{
577		// shouldn't happen
578	0	continue;
579		}
580	0	boolean sourceChanged = !source.equals(lastSource);
581	0	if (sourceChanged)
582		{
583	0	lineLength = 0;
584	0	countForSource = 0;
585	0	sourceCount++;
586		}
587	0	if (sourceCount > MAX_SOURCES && summary)
588		{
589	0	ellipsis = true;
590	0	moreSources = true;
591	0	break;
592		}
593	0	lastSource = source;
594	0	countForSource++;
595	0	if (countForSource == 1 || !summary)
596		{
597	0	sb.append("<br/>\n");
598		}
599	0	if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
600		{
601	0	String accessionId = ref.getAccessionId();
602	0	lineLength += accessionId.length() + 1;
603	0	if (countForSource > 1 && summary)
604		{
605	0	sb.append(",\n ").append(accessionId);
606	0	lineLength++;
607		}
608		else
609		{
610	0	sb.append(source).append(" ").append(accessionId);
611	0	lineLength += source.length();
612		}
613	0	maxLineLength = Math.max(maxLineLength, lineLength);
614		}
615	0	if (countForSource == MAX_REFS_PER_SOURCE && summary)
616		{
617	0	sb.append(COMMA).append(ELLIPSIS);
618	0	ellipsis = true;
619		}
620		}
621	0	if (moreSources)
622		{
623	0	sb.append("<br/>\n").append(source).append(COMMA).append(ELLIPSIS);
624		}
625	0	if (ellipsis)
626		{
627	0	sb.append("<br/>\n(");
628	0	sb.append(MessageManager.getString("label.output_seq_details"));
629	0	sb.append(")");
630		}
631
632	0	return maxLineLength;
633		}
634
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
635	0	public void createTooltipAnnotationReport(final StringBuilder tip,...
636		SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
637		FeatureRendererModel fr)
638		{
639	0	int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs,
640		showNpFeats, fr, true);
641
642	0	if (maxWidth > 60)
643		{
644		// ? not sure this serves any useful purpose
645		// tip.insert(0, "<table width=350 border=0><tr><td>");
646		// tip.append("</td></tr></table>");
647		}
648		}
649		}