Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Sequencefeature	46	149	49	0.00%	Show methods

Class Sequencefeature

Class Sequencefeature	Line # 46	Total Statements 149	Complexity 49	TOTAL Coverage 0.00%
Sequencefeature(VamsasAppDatastore,SequenceFeature,uk.ac.vamsas.objects.core.DataSet,uk.ac.vamsas.objects.core.Sequence)   Sequencefeature(VamsasAppDatastore,SequenceFeature,uk.ac.vamsas.objects.core.DataSet,uk.ac.vamsas.objects.core.Sequence)	5555	4.04	1.01	0.0 0.00%
Sequencefeature(VamsasAppDatastore,DataSetAnnotations,SequenceI)   Sequencefeature(VamsasAppDatastore,DataSetAnnotations,SequenceI)	6666	3.03	1.01	0.0 0.00%
addToDocument() : void   addToDocument() : void	7575	9.09	2.02	0.0 0.00%
addFromDocument() : void   addFromDocument() : void	9494	8.08	2.02	0.0 0.00%
conflict() : void   conflict() : void	110110	7.07	1.01	0.0 0.00%
updateToDoc() : void   updateToDoc() : void	123123	11.011	3.03	0.0 0.00%
updateFromDoc() : void   updateFromDoc() : void	149149	12.012	3.03	0.0 0.00%
getDSAnnotationFromJalview(RangeAnnotation,jalview.datamodel.SequenceFeature) : RangeAnnotation   getDSAnnotationFromJalview(RangeAnnotation,jalview.datamodel.SequenceFeature) : RangeAnnotation	190190	50.050	16.016	0.0 0.00%
getJalviewSeqFeature(RangeAnnotation) : SequenceFeature   getJalviewSeqFeature(RangeAnnotation) : SequenceFeature	280280	45.045	20.020	0.0 0.00%

 

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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.vamsas;
22
23		import jalview.bin.Console;
24		import jalview.datamodel.SequenceFeature;
25		import jalview.datamodel.SequenceI;
26		import jalview.io.VamsasAppDatastore;
27		import jalview.util.UrlLink;
28
29		import java.util.Enumeration;
30		import java.util.Iterator;
31		import java.util.Vector;
32
33		import uk.ac.vamsas.objects.core.DataSetAnnotations;
34		import uk.ac.vamsas.objects.core.Link;
35		import uk.ac.vamsas.objects.core.Property;
36		import uk.ac.vamsas.objects.core.Provenance;
37		import uk.ac.vamsas.objects.core.RangeAnnotation;
38		import uk.ac.vamsas.objects.core.Score;
39		import uk.ac.vamsas.objects.core.Seg;
40		import uk.ac.vamsas.objects.utils.Properties;
41
42		/**
43		* @author JimP
44		*
45		*/
		0% Uncovered Elements: 228 (228) Complexity: 49 Complexity Density: 0.33
46		public class Sequencefeature extends Rangetype
47		{
48
49		uk.ac.vamsas.objects.core.DataSet dataset;
50
51		uk.ac.vamsas.objects.core.Sequence sequence;
52
53		private SequenceI dsSeq;
54
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
55	0	public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,...
56		SequenceFeature sequenceFeature,
57		uk.ac.vamsas.objects.core.DataSet dataset,
58		uk.ac.vamsas.objects.core.Sequence sequence)
59		{
60	0	super(vamsasAppDatastore, sequenceFeature, DataSetAnnotations.class);
61	0	this.dataset = dataset;
62	0	this.sequence = sequence;
63	0	doSync();
64		}
65
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
66	0	public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,...
67		DataSetAnnotations dseta, SequenceI dsSeq)
68		{
69	0	super(vamsasAppDatastore, dseta,
70		jalview.datamodel.SequenceFeature.class);
71	0	this.dsSeq = dsSeq;
72	0	doJvUpdate();
73		}
74
		0% Uncovered Elements: 11 (11) Complexity: 2 Complexity Density: 0.22
75	0	@Override...
76		public void addToDocument()
77		{
78	0	DataSetAnnotations dsa = (DataSetAnnotations) vobj;
79	0	jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
80	0	dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
81		new DataSetAnnotations(), feature);
82	0	if (dsa.getProvenance() == null)
83		{
84	0	dsa.setProvenance(new Provenance());
85		}
86	0	addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
87		// to update
88	0	dsa.addSeqRef(sequence); // we have just created this annotation
89		// - so safe to use this
90	0	bindjvvobj(feature, dsa);
91	0	dataset.addDataSetAnnotations(dsa);
92		}
93
		0% Uncovered Elements: 10 (10) Complexity: 2 Complexity Density: 0.25
94	0	@Override...
95		public void addFromDocument()
96		{
97	0	DataSetAnnotations dsa = (DataSetAnnotations) vobj;
98	0	if (dsa.getSeqRefCount() != 1)
99		{
100	0	Console.warn("Not binding " + dsa.getVorbaId()
101		+ " to Sequence Feature - has multiple dataset sequence references.");
102	0	return;
103		}
104	0	jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
105	0	dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));
106	0	jvobj = sf;
107	0	bindjvvobj(sf, dsa);
108		}
109
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
110	0	@Override...
111		public void conflict()
112		{
113	0	log.warn("Untested sequencefeature conflict code");
114	0	DataSetAnnotations dsa = (DataSetAnnotations) vobj;
115	0	jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
116	0	jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);
117	0	replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature
118		// to newly created feature
119	0	dsSeq.addSequenceFeature(sf); // add new imported feature
120	0	addToDocument(); // and create a new feature in the document
121		}
122
		0% Uncovered Elements: 15 (15) Complexity: 3 Complexity Density: 0.27
123	0	@Override...
124		public void updateToDoc()
125		{
126	0	DataSetAnnotations dsa = (DataSetAnnotations) vobj;
127	0	jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
128	0	if (dsa.getSeqRefCount() != 1)
129		{
130	0	replaceJvObjMapping(feature, null);
131	0	Console.warn(
132		"Binding of annotation to jalview feature has changed. Removing binding and recreating.");
133	0	doSync(); // re-verify bindings.
134		}
135		else
136		{
137		// Sync the features from Jalview
138	0	long oldref = dsa.get__last_hash();
139	0	getDSAnnotationFromJalview(dsa, feature);
140	0	if (oldref != dsa.hashCode())
141		{
142	0	Console.debug("Updated dataset sequence annotation from feature.");
143	0	addProvenance(dsa.getProvenance(), "modified");
144		}
145		}
146
147		}
148
		0% Uncovered Elements: 16 (16) Complexity: 3 Complexity Density: 0.25
149	0	@Override...
150		public void updateFromDoc()
151		{
152	0	DataSetAnnotations dsa = (DataSetAnnotations) vobj;
153	0	jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
154	0	if (dsa.getSeqRefCount() != 1)
155		{
156		// conflicting update from document - we cannot map this feature anymore.
157	0	replaceJvObjMapping(feature, null);
158	0	Console.warn("annotation (" + dsa.getVorbaId()
159		+ " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
160		// - consider deleting the feature ?
161	0	dsSeq.deleteFeature(feature);
162		// doSync();
163		}
164		else
165		{
166		// Sync the features to Jalview - easiest to delete and add the feature
167		// again
168	0	jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);
169	0	dsSeq.deleteFeature(feature);
170	0	replaceJvObjMapping(feature, newsf);
171	0	dsSeq.addSequenceFeature(newsf);
172	0	if (feature.otherDetails != null)
173		{
174		// TODO later: leave this to finalise method ?
175	0	feature.otherDetails.clear();
176		}
177		}
178		}
179
180		/**
181		* correctly create/update a RangeAnnotation from a jalview sequence feature
182		* TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class
183		*
184		* @param dsa
185		* (typically DataSetAnnotations or AlignmentSequenceAnnotation)
186		* @param feature
187		* (the feature to be mapped from)
188		* @return
189		*/
		0% Uncovered Elements: 76 (76) Complexity: 16 Complexity Density: 0.32
190	0	private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,...
191		jalview.datamodel.SequenceFeature feature)
192		{
193	0	dsa.setType(feature.getType());
194	0	Seg vSeg = new Seg();
195	0	vSeg.setStart(feature.getBegin());
196	0	vSeg.setEnd(feature.getEnd());
197	0	vSeg.setInclusive(true);
198	0	if (dsa.getSegCount() > 1)
199		{
200	0	Console.debug(
201		"About to destroy complex annotation in vamsas document mapped to sequence feature ("
202		+ dsa.getVorbaId() + ")");
203		}
204	0	dsa.setSeg(new Seg[] { vSeg });
205	0	dsa.setDescription(feature.getDescription());
206	0	dsa.setStatus(feature.getStatus());
207	0	if (feature.links != null && feature.links.size() > 0)
208		{
209	0	for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
210		{
211	0	String link = feature.links.elementAt(i);
212	0	UrlLink ulink = new UrlLink(link);
213	0	if (ulink.isValid())
214		{
215		// We only add static links to the document.
216	0	Link vLink = new Link();
217	0	vLink.setContent(ulink.getLabel());
218	0	vLink.setHref(ulink.getTarget());
219	0	dsa.addLink(vLink);
220		}
221		}
222		}
223	0	dsa.setGroup(feature.getFeatureGroup());
224	0	if (!Float.isNaN(feature.getScore()))
225		{
226	0	Score fscore = new Score();
227	0	dsa.setScore(new Score[] { fscore });
228	0	fscore.setContent(feature.getScore());
229	0	fscore.setName(feature.getType());
230		}
231	0	if (feature.otherDetails != null)
232		{
233	0	Iterator<String> iter = feature.otherDetails.keySet().iterator();
234	0	Vector props = dsa.getPropertyAsReference();
235	0	while (iter.hasNext())
236		{
237	0	String key = iter.next();
238	0	if (!key.equalsIgnoreCase("score")
239		&& !key.equalsIgnoreCase("status"))
240		{
241	0	Property nprop = new Property();
242	0	nprop.setName(key);
243	0	Object vlu = feature.getValue(key);
244	0	nprop.setContent(feature.getValue(key).toString());
245	0	boolean valid = false;
246	0	if (vlu instanceof String)
247		{
248	0	nprop.setType(uk.ac.vamsas.objects.utils.Properties.STRINGTYPE);
249	0	valid = true;
250		}
251	0	else if (vlu instanceof Integer)
252		{
253	0	valid = true;
254	0	nprop.setType(
255		uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
256		}
257	0	else if (vlu instanceof Float)
258		{
259	0	nprop.setType(uk.ac.vamsas.objects.utils.Properties.FLOATTYPE);
260	0	valid = true;
261		}
262	0	if (valid)
263		{
264	0	if (props != null)
265		{
266	0	uk.ac.vamsas.objects.utils.Properties.addOrReplace(props,
267		nprop);
268		}
269		else
270		{
271	0	dsa.addProperty(nprop);
272		}
273		}
274		}
275		}
276		}
277	0	return dsa;
278		}
279
		0% Uncovered Elements: 77 (77) Complexity: 20 Complexity Density: 0.44
280	0	private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)...
281		{
282	0	int[] se = getBounds(dseta);
283
284		/*
285		* try to identify feature score
286		*/
287	0	boolean scoreFound = false;
288	0	float theScore = 0f;
289	0	String featureType = dseta.getType();
290	0	if (dseta.getScoreCount() > 0)
291		{
292	0	Enumeration scr = dseta.enumerateScore();
293	0	while (scr.hasMoreElements())
294		{
295	0	Score score = (Score) scr.nextElement();
296	0	if (score.getName().equals(featureType))
297		{
298	0	theScore = score.getContent();
299	0	scoreFound = true;
300		}
301		}
302		}
303
304	0	SequenceFeature sf = null;
305	0	if (scoreFound)
306		{
307	0	sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
308		se[1], theScore, dseta.getGroup());
309		}
310		else
311		{
312	0	sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
313		se[1], dseta.getGroup());
314		}
315	0	sf.setStatus(dseta.getStatus());
316	0	if (dseta.getLinkCount() > 0)
317		{
318	0	Link[] links = dseta.getLink();
319	0	for (int i = 0; i < links.length; i++)
320		{
321		// TODO: use URLLink parsing/validation here.
322	0	sf.addLink(links[i].getContent() + "|" + links[i].getHref());
323		}
324		}
325	0	if (dseta.getScoreCount() > 0)
326		{
327	0	Enumeration scr = dseta.enumerateScore();
328	0	while (scr.hasMoreElements())
329		{
330	0	Score score = (Score) scr.nextElement();
331	0	if (!score.getName().equals(sf.getType()))
332		{
333	0	sf.setValue(score.getName(), "" + score.getContent());
334		}
335		}
336		}
337		// other details
338	0	Enumeration props = dseta.enumerateProperty();
339	0	while (props.hasMoreElements())
340		{
341	0	Property p = (Property) props.nextElement();
342	0	Object val = null;
343	0	if (Properties.isValid(p))
344		{
345	0	if (Properties.isString(p))
346		{
347	0	val = p.getContent();
348		}
349	0	if (Properties.isBoolean(p))
350		{
351	0	try
352		{
353	0	val = Boolean.valueOf(p.getContent());
354		} catch (Exception e)
355		{
356		}
357		}
358	0	if (Properties.isFloat(p))
359		{
360	0	try
361		{
362	0	val = Float.valueOf(p.getContent());
363
364		} catch (Exception e)
365		{
366		}
367		}
368	0	if (Properties.isInteger(p))
369		{
370	0	try
371		{
372	0	val = Integer.valueOf(p.getContent());
373		} catch (Exception e)
374		{
375		}
376		}
377	0	if (val != null)
378		{
379	0	sf.setValue(p.getName(), val);
380		}
381		}
382		}
383
384	0	return sf;
385		}
386
387		}