Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Datasetsequence	42	87	34	0.00%	Show methods

Class Datasetsequence

Class Datasetsequence	Line # 42	Total Statements 87	Complexity 34	TOTAL Coverage 0.00%
Datasetsequence(VamsasAppDatastore,SequenceI,String,DataSet)   Datasetsequence(VamsasAppDatastore,SequenceI,String,DataSet)	5050	4.04	1.01	0.0 0.00%
Datasetsequence(VamsasAppDatastore,Sequence)   Datasetsequence(VamsasAppDatastore,Sequence)	6060	2.02	1.01	0.0 0.00%
addFromDocument() : void   addFromDocument() : void	6767	7.07	1.01	0.0 0.00%
updateFromDoc() : void   updateFromDoc() : void	8080	17.017	10.010	0.0 0.00%
updateSqFeatures() : boolean   updateSqFeatures() : boolean	135135	6.06	1.01	0.0 0.00%
addToDocument() : void   addToDocument() : void	151151	14.014	1.01	0.0 0.00%
updateDbRefs() : boolean   updateDbRefs() : boolean	175175	7.07	4.04	0.0 0.00%
updateJvDbRefs() : boolean   updateJvDbRefs() : boolean	203203	8.08	3.03	0.0 0.00%
conflict() : void   conflict() : void	223223	2.02	1.01	0.0 0.00%
updateToDoc() : void   updateToDoc() : void	234234	19.019	10.010	0.0 0.00%
getModified() : boolean   getModified() : boolean	279279	1.01	1.01	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.datamodel.DBRefEntry;
24		import jalview.datamodel.SequenceFeature;
25		import jalview.datamodel.SequenceI;
26		import jalview.io.VamsasAppDatastore;
27
28		import java.util.List;
29
30		import uk.ac.vamsas.objects.core.DataSet;
31		import uk.ac.vamsas.objects.core.DbRef;
32		import uk.ac.vamsas.objects.core.Sequence;
33
34		/**
35		* synchronize a vamsas dataset sequence with a jalview dataset sequence. This
36		* class deals with all sequence features and database references associated
37		* with the jalview sequence.
38		*
39		* @author JimP
40		*
41		*/
		0% Uncovered Elements: 126 (126) Complexity: 34 Complexity Density: 0.39
42		public class Datasetsequence extends DatastoreItem
43		{
44		String dict;
45
46		private DataSet dataset;
47
48		// private AlignmentI jvdset;
49
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
50	0	public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,...
51		SequenceI sq, String theDict, DataSet theDataset)
52		{
53	0	super(vamsasAppDatastore, sq, uk.ac.vamsas.objects.core.Sequence.class);
54	0	this.dataset = theDataset;
55		// this.jvdset = jvdset;
56	0	this.dict = theDict;
57	0	doSync();
58		}
59
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
60	0	public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,...
61		Sequence vdseq)
62		{
63	0	super(vamsasAppDatastore, vdseq, SequenceI.class);
64	0	doJvUpdate();
65		}
66
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
67	0	@Override...
68		public void addFromDocument()
69		{
70	0	Sequence vseq = (Sequence) vobj;
71	0	SequenceI dsseq = new jalview.datamodel.Sequence(vseq.getName(),
72		vseq.getSequence(), (int) vseq.getStart(), (int) vseq.getEnd());
73	0	dsseq.setDescription(vseq.getDescription());
74	0	bindjvvobj(dsseq, vseq);
75	0	dsseq.setVamsasId(vseq.getVorbaId().getId());
76	0	jvobj = dsseq;
77	0	modified = true;
78		}
79
		0% Uncovered Elements: 27 (27) Complexity: 10 Complexity Density: 0.59
80	0	@Override...
81		public void updateFromDoc()
82		{
83	0	Sequence sq = (Sequence) vobj;
84	0	SequenceI sequence = (SequenceI) jvobj;
85	0	if (!sequence.getSequenceAsString().equals(sq.getSequence()))
86		{
87	0	log.warn(
88		"Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
89		}
90		else
91		{
92		// verify and update principal attributes.
93	0	if (sequence.getDescription() != null
94		&& (sequence.getDescription() == null || !sequence
95		.getDescription().equals(sq.getDescription())))
96		{
97	0	sequence.setDescription(sq.getDescription());
98	0	modified = true;
99		}
100	0	if (sequence.getSequence() == null
101		|| !sequence.getSequenceAsString().equals(sq.getSequence()))
102		{
103	0	if (sequence.getStart() != sq.getStart()
104		|| sequence.getEnd() != sq.getEnd())
105		{
106		// update modified sequence.
107	0	sequence.setSequence(sq.getSequence());
108	0	sequence.setStart((int) sq.getStart());
109	0	sequence.setEnd((int) sq.getEnd());
110	0	modified = true;
111		}
112		}
113	0	if (!sequence.getName().equals(sq.getName()))
114		{
115	0	sequence.setName(sq.getName());
116	0	modified = true;
117		}
118	0	modified |= updateJvDbRefs();
119		// updateJvFeatures();
120		}
121		}
122
123		/*
124		* private void updateJvFeatures() { Sequence vsq = (Sequence) vobj;
125		*
126		* // add or update any new features/references on dataset sequence if
127		* (vsq.getgetSequenceFeatures() != null) { int sfSize =
128		* sq.getSequenceFeatures().length;
129		*
130		* for (int sf = 0; sf < sfSize; sf++) { new
131		* jalview.io.vamsas.Sequencefeature(datastore,
132		* (jalview.datamodel.SequenceFeature) sq .getSequenceFeatures()[sf], dataset,
133		* (Sequence) vobj); } } }
134		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
135	0	private boolean updateSqFeatures()...
136		{
137	0	boolean changed = false;
138	0	SequenceI sq = (SequenceI) jvobj;
139
140		// add or update any new features/references on dataset sequence
141	0	List<SequenceFeature> sfs = sq.getSequenceFeatures();
142	0	for (SequenceFeature sf : sfs)
143		{
144	0	changed |= new jalview.io.vamsas.Sequencefeature(datastore, sf,
145		dataset, (Sequence) vobj).docWasUpdated();
146		}
147
148	0	return changed;
149		}
150
		0% Uncovered Elements: 14 (14) Complexity: 1 Complexity Density: 0.07
151	0	@Override...
152		public void addToDocument()
153		{
154	0	SequenceI sq = (SequenceI) jvobj;
155	0	Sequence sequence = new Sequence();
156	0	bindjvvobj(sq, sequence);
157	0	sq.setVamsasId(sequence.getVorbaId().getId());
158	0	sequence.setSequence(sq.getSequenceAsString());
159	0	sequence.setDictionary(dict);
160	0	sequence.setName(sq.getName());
161	0	sequence.setStart(sq.getStart());
162	0	sequence.setEnd(sq.getEnd());
163	0	sequence.setDescription(sq.getDescription());
164	0	dataset.addSequence(sequence);
165	0	vobj = sequence;
166	0	updateSqFeatures();
167	0	updateDbRefs();// sq,(Sequence) vobj, dataset);
168		}
169
170		/**
171		* sync database references from jv to document
172		*
173		* @return true if document was modified
174		*/
		0% Uncovered Elements: 11 (11) Complexity: 4 Complexity Density: 0.57
175	0	private boolean updateDbRefs()...
176		{
177	0	boolean modifiedthedoc = false;
178	0	SequenceI sq = (SequenceI) jvobj;
179
180	0	if (sq.getDatasetSequence() == null && sq.getDBRefs() != null)
181		{
182		// only sync database references for dataset sequences
183	0	List<DBRefEntry> entries = sq.getDBRefs();
184		// jalview.datamodel.DBRefEntry dbentry;
185	0	for (int db = 0, dn = entries.size(); db < dn; db++)
186		{
187	0	modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
188		// dbentry =
189		entries.get(db), sq, (Sequence) vobj, dataset)
190		.docWasUpdated();
191
192		}
193
194		}
195	0	return modifiedthedoc;
196		}
197
198		/**
199		* sync database references from document to jv sequence
200		*
201		* @return true if local sequence refs were modified
202		*/
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
203	0	private boolean updateJvDbRefs()...
204		{
205	0	boolean modifiedtheseq = false;
206	0	SequenceI sq = (SequenceI) jvobj;
207	0	Sequence vsq = (Sequence) vobj;
208	0	if (vsq.getDbRefCount() > 0)
209		{
210		// only sync database references for dataset sequences
211	0	DbRef[] entries = vsq.getDbRef();
212		// DbRef dbentry;
213	0	for (int db = 0; db < entries.length; db++)
214		{
215	0	modifiedtheseq |= new jalview.io.vamsas.Dbref(datastore,
216		// dbentry =
217		entries[db], vsq, sq).jvWasUpdated();
218		}
219		}
220	0	return modifiedtheseq;
221		}
222
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
223	0	@Override...
224		public void conflict()
225		{
226	0	log.warn(
227		"Conflict in dataset sequence update to document. Overwriting document");
228		// TODO: could try to import from document data to jalview first. and then
229	0	updateToDoc();
230		}
231
232		boolean modified = false;
233
		0% Uncovered Elements: 29 (29) Complexity: 10 Complexity Density: 0.53
234	0	@Override...
235		public void updateToDoc()
236		{
237	0	SequenceI sq = (SequenceI) jvobj;
238	0	Sequence sequence = (Sequence) vobj;
239		// verify and update principal attributes.
240	0	if (sequence.getDescription() != null
241		&& (sequence.getDescription() == null || !sequence
242		.getDescription().equals(sq.getDescription())))
243		{
244	0	sequence.setDescription(sq.getDescription());
245	0	modified = true;
246		}
247	0	if (sequence.getSequence() == null
248		|| !sequence.getSequence().equals(sq.getSequenceAsString()))
249		{
250	0	if (sequence.getStart() != sq.getStart()
251		|| sequence.getEnd() != sq.getEnd())
252		{
253		// update modified sequence.
254	0	sequence.setSequence(sq.getSequenceAsString());
255	0	sequence.setStart(sq.getStart());
256	0	sequence.setEnd(sq.getEnd());
257	0	modified = true;
258		}
259		}
260	0	if (!dict.equals(sequence.getDictionary()))
261		{
262	0	sequence.setDictionary(dict);
263	0	modified = true;
264		}
265	0	if (!sequence.getName().equals(sq.getName()))
266		{
267	0	sequence.setName(sq.getName());
268	0	modified = true;
269		}
270	0	modified |= updateDbRefs();
271	0	modified |= updateSqFeatures();
272		}
273
274		/**
275		* (probably could just do vobj.isModified(), but..)
276		*
277		* @return true if document's dataset sequence was modified
278		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
279	0	public boolean getModified()...
280		{
281	0	return modified;
282		}
283
284		}