Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Dbref	33	73	25	0.00%	Show methods

Class Dbref

Class Dbref	Line # 33	Total Statements 73	Complexity 25	TOTAL Coverage 0.00%
Dbref(VamsasAppDatastore,DBRefEntry,jalview.datamodel.SequenceI,uk.ac.vamsas.objects.core.Sequence,DataSet)   Dbref(VamsasAppDatastore,DBRefEntry,jalview.datamodel.SequenceI,uk.ac.vamsas.objects.core.Sequence,DataSet)	4141	6.06	1.01	0.0 0.00%
Dbref(VamsasAppDatastore,DbRef,Sequence,SequenceI)   Dbref(VamsasAppDatastore,DbRef,Sequence,SequenceI)	5555	5.05	1.01	0.0 0.00%
updateToDoc() : void   updateToDoc() : void	6565	17.017	4.04	0.0 0.00%
updateMapTo(jalview.datamodel.Mapping) : void   updateMapTo(jalview.datamodel.Mapping) : void	108108	7.07	7.07	0.0 0.00%
updateFromDoc() : void   updateFromDoc() : void	149149	11.011	5.05	0.0 0.00%
conflict() : void   conflict() : void	174174	3.03	1.01	0.0 0.00%
addFromDocument() : void   addFromDocument() : void	184184	9.09	3.03	0.0 0.00%
addToDocument() : void   addToDocument() : void	210210	15.015	3.03	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.DBRefEntry;
25		import jalview.datamodel.SequenceI;
26		import jalview.io.VamsasAppDatastore;
27
28		import uk.ac.vamsas.objects.core.DataSet;
29		import uk.ac.vamsas.objects.core.DbRef;
30		import uk.ac.vamsas.objects.core.Map;
31		import uk.ac.vamsas.objects.core.Sequence;
32
		0% Uncovered Elements: 111 (111) Complexity: 25 Complexity Density: 0.34
33		public class Dbref extends Rangetype
34		{
35		jalview.datamodel.SequenceI sq = null;
36
37		uk.ac.vamsas.objects.core.Sequence sequence = null;
38
39		DataSet ds;
40
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
41	0	public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,...
42		jalview.datamodel.SequenceI sq2,
43		uk.ac.vamsas.objects.core.Sequence sequence2, DataSet dataset)
44		{
45	0	super(datastore, dbentry, DbRef.class);
46		// initialise object specific attributes
47	0	sq = sq2;
48	0	sequence = sequence2;
49	0	this.jvobj = dbentry;
50	0	ds = dataset;
51		// call the accessors
52	0	doSync();
53		}
54
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
55	0	public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,...
56		SequenceI dsseq)
57		{
58	0	super(datastore, ref, jalview.datamodel.DBRefEntry.class);
59	0	sequence = vdseq;
60	0	sq = dsseq;
61	0	ds = (DataSet) vdseq.getV_parent();
62	0	doJvUpdate();
63		}
64
		0% Uncovered Elements: 23 (23) Complexity: 4 Complexity Density: 0.24
65	0	public void updateToDoc()...
66		{
67	0	DbRef dbref = (DbRef) this.vobj;
68	0	DBRefEntry jvobj = (DBRefEntry) this.jvobj;
69	0	dbref.setAccessionId(jvobj.getAccessionId());
70	0	dbref.setSource(jvobj.getSource());
71	0	dbref.setVersion(jvobj.getVersion());
72	0	if (jvobj.getMap() != null)
73		{
74		// Record mapping to external database coordinate system.
75	0	jalview.datamodel.Mapping mp = jvobj.getMap();
76	0	if (mp.getMap() != null)
77		{
78	0	Map vMap = null;
79	0	if (dbref.getMapCount() == 0)
80		{
81	0	vMap = new Map();
82	0	initMapType(vMap, mp.getMap(), true);
83	0	dbref.addMap(vMap);
84		}
85		else
86		{
87		// we just update the data anyway.
88	0	vMap = dbref.getMap(0);
89	0	initMapType(vMap, mp.getMap(), true);
90		}
91	0	updateMapTo(mp);
92		}
93		}
94		else
95		{
96	0	Console.debug(
97		"Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
98		}
99
100		}
101
102		/**
103		* ugly hack to try to get the embedded sequences within a database reference
104		* to be stored in the document's dataset.
105		*
106		* @param mp
107		*/
		0% Uncovered Elements: 17 (17) Complexity: 7 Complexity Density: 1
108	0	private void updateMapTo(jalview.datamodel.Mapping mp)...
109		{
110	0	log.info(
111		"Performing updateMapTo remove this message when we know what we're doing.");
112		// TODO determine how sequences associated with database mappings are stored
113		// in the document
114	0	if (mp != null && mp.getTo() != null)
115		{
116	0	if (mp.getTo().getDatasetSequence() == null)
117		{
118		// TODO: fix this hinky sh!t
119	0	DatastoreItem dssync = dsReg.getDatastoreItemFor(mp.getTo());
120	0	if (dssync == null)
121		{
122		// sync the dataset sequence, if it hasn't been done already.
123		// TODO: ensure real dataset sequence corresponding to getTo is
124		// recovered
125	0	dssync = new Datasetsequence(datastore, mp.getTo(),
126	0	(mp.getMappedWidth() == mp.getWidth())
127		? sequence.getDictionary()
128	0	: ((mp.getMappedWidth() == 3)
129		? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
130		: uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA),
131		ds);
132		}
133		//
134		// TODO: NOW add a mapping between new dataset sequence and sequence
135		// associated with the database reference
136
137		// dna mappings only...
138		// new jalview.io.vamsas.Sequencemapping(datastore, mp, sequence, ds);
139
140		}
141
142		}
143		else
144		{
145	0	log.debug("Ignoring non-dataset sequence mapping.");
146		}
147		}
148
		0% Uncovered Elements: 17 (17) Complexity: 5 Complexity Density: 0.45
149	0	public void updateFromDoc()...
150		{
151	0	DbRef vobj = (DbRef) this.vobj;
152	0	DBRefEntry jvobj = (DBRefEntry) this.jvobj;
153	0	jvobj.setAccessionId(vobj.getAccessionId());
154	0	jvobj.setSource(vobj.getSource());
155	0	jvobj.setVersion(vobj.getVersion());
156		// add new dbref
157	0	if (vobj.getMapCount() > 0)
158		{
159		// TODO: Jalview ignores all the other maps
160	0	if (vobj.getMapCount() > 1)
161		{
162	0	Console.debug("Ignoring additional mappings on DbRef: "
163		+ jvobj.getSource() + ":" + jvobj.getAccessionId());
164		}
165	0	jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
166		parsemapType(vobj.getMap(0)));
167	0	if (jvobj.getMap() == null || !mp.equals(jvobj.getMap()))
168		{
169	0	jvobj.setMap(mp);
170		}
171		}
172		}
173
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
174	0	public void conflict()...
175		{
176	0	DbRef vobj = (DbRef) this.vobj;
177	0	DBRefEntry jvobj = (DBRefEntry) this.jvobj;
178	0	Console.debug("Conflict in dbentry update for " + vobj.getAccessionId()
179		+ vobj.getSource() + " " + vobj.getVorbaId());
180		// TODO Auto-generated method stub
181
182		}
183
		0% Uncovered Elements: 13 (13) Complexity: 3 Complexity Density: 0.33
184	0	public void addFromDocument()...
185		{
186	0	DbRef vobj = (DbRef) this.vobj;
187	0	DBRefEntry jvobj = (DBRefEntry) this.jvobj;
188		// add new dbref
189	0	sq.addDBRef(jvobj = new jalview.datamodel.DBRefEntry(
190		vobj.getSource().toString(), vobj.getVersion().toString(),
191		vobj.getAccessionId().toString()));
192	0	if (vobj.getMapCount() > 0)
193		{
194		// TODO: Jalview ignores all the other maps
195	0	if (vobj.getMapCount() > 1)
196		{
197	0	Console.debug("Ignoring additional mappings on DbRef: "
198		+ jvobj.getSource() + ":" + jvobj.getAccessionId());
199		}
200	0	jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
201		parsemapType(vobj.getMap(0)));
202	0	jvobj.setMap(mp);
203		}
204		// TODO: jalview ignores links and properties because it doesn't know what
205		// to do with them.
206
207	0	bindjvvobj(jvobj, vobj);
208		}
209
		0% Uncovered Elements: 19 (19) Complexity: 3 Complexity Density: 0.2
210	0	public void addToDocument()...
211		{
212	0	DBRefEntry jvobj = (DBRefEntry) this.jvobj;
213	0	DbRef dbref = new DbRef();
214	0	bindjvvobj(jvobj, dbref);
215	0	dbref.setAccessionId(jvobj.getAccessionId());
216	0	dbref.setSource(jvobj.getSource());
217	0	dbref.setVersion(jvobj.getVersion());
218	0	sequence.addDbRef(dbref);
219	0	if (jvobj.getMap() != null)
220		{
221	0	jalview.datamodel.Mapping mp = jvobj.getMap();
222	0	if (mp.getMap() != null)
223		{
224	0	Map vMap = new Map();
225	0	initMapType(vMap, mp.getMap(), true);
226	0	dbref.addMap(vMap);
227	0	updateMapTo(mp);
228		}
229		else
230		{
231	0	Console.debug(
232		"Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
233		}
234		}
235		}
236
237		}