Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Sequencemapping	53	135	65	0.00%	Show methods

Class Sequencemapping

Class Sequencemapping	Line # 53	Total Statements 135	Complexity 65	TOTAL Coverage 0.00%
Sequencemapping(VamsasAppDatastore,SequenceMapping)   Sequencemapping(VamsasAppDatastore,SequenceMapping)	5555	2.02	1.01	0.0 0.00%
Sequencemapping(VamsasAppDatastore,jalview.datamodel.Mapping,uk.ac.vamsas.objects.core.SequenceType,uk.ac.vamsas.objects.core.DataSet)   Sequencemapping(VamsasAppDatastore,jalview.datamodel.Mapping,uk.ac.vamsas.objects.core.SequenceType,uk.ac.vamsas.objects.core.DataSet)	7777	6.06	1.01	0.0 0.00%
validate() : void   validate() : void	9393	7.07	7.07	0.0 0.00%
addToDocument() : void   addToDocument() : void	114114	1.01	1.01	0.0 0.00%
addFromDocument() : void   addFromDocument() : void	119119	1.01	1.01	0.0 0.00%
conflict() : void   conflict() : void	124124	1.01	1.01	0.0 0.00%
updateToDoc() : void   updateToDoc() : void	130130	1.01	1.01	0.0 0.00%
updateFromDoc() : void   updateFromDoc() : void	135135	1.01	1.01	0.0 0.00%
conflict(Mapping,SequenceMapping) : void   conflict(Mapping,SequenceMapping) : void	140140	1.01	1.01	0.0 0.00%
add(Mapping,uk.ac.vamsas.objects.core.SequenceType,DataSet) : void   add(Mapping,uk.ac.vamsas.objects.core.SequenceType,DataSet) : void	146146	32.032	10.010	0.0 0.00%
<init>, line 234()   <init>, line 234()	234234	1.01	1.01	0.0 0.00%
update(SequenceMapping,jalview.datamodel.Mapping) : void   update(SequenceMapping,jalview.datamodel.Mapping) : void	238238	1.01	1.01	0.0 0.00%
update(jalview.datamodel.Mapping,SequenceMapping) : void   update(jalview.datamodel.Mapping,SequenceMapping) : void	244244	1.01	1.01	0.0 0.00%
add(SequenceMapping) : void   add(SequenceMapping) : void	257257	48.048	17.017	0.0 0.00%
matchConjugateDBRefs(SequenceI,SequenceI,jalview.util.MapList) : void   matchConjugateDBRefs(SequenceI,SequenceI,jalview.util.MapList) : void	385385	31.031	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.AlignedCodonFrame;
25		import jalview.datamodel.AlignmentI;
26		import jalview.datamodel.DBRefEntry;
27		import jalview.datamodel.Mapping;
28		import jalview.datamodel.SequenceI;
29		import jalview.gui.Desktop;
30		import jalview.io.VamsasAppDatastore;
31
32		import java.util.ArrayList;
33		import java.util.List;
34		import java.util.Vector;
35
36		import uk.ac.vamsas.objects.core.AlignmentSequence;
37		import uk.ac.vamsas.objects.core.DataSet;
38		import uk.ac.vamsas.objects.core.Sequence;
39		import uk.ac.vamsas.objects.core.SequenceMapping;
40		import uk.ac.vamsas.objects.core.SequenceType;
41
42		/**
43		* binds a vamsas sequence mapping object from the vamsas document to a maplist
44		* object associated with a mapping in the Jalview model. We use the maplist
45		* object because these are referred to both in the Mapping object associated
46		* with a jalview.datamodel.DBRefEntry and in the array of
47		* jalview.datamodel.AlCodonFrame objects that Jalview uses to propagate
48		* sequence mapping position highlighting across the views.
49		*
50		* @author JimP
51		*
52		*/
		0% Uncovered Elements: 228 (228) Complexity: 65 Complexity Density: 0.48
53		public class Sequencemapping extends Rangetype
54		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
55	0	public Sequencemapping(VamsasAppDatastore datastore,...
56		SequenceMapping sequenceMapping)
57		{
58	0	super(datastore, sequenceMapping, jalview.util.MapList.class);
59	0	doJvUpdate();
60		}
61
62		private SequenceType from;
63
64		private DataSet ds;
65
66		private Mapping mjvmapping;
67
68		/**
69		* create or update a vamsas sequence mapping corresponding to a jalview
70		* Mapping between two dataset sequences
71		*
72		* @param datastore
73		* @param mjvmapping
74		* @param from
75		* @param ds
76		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
77	0	public Sequencemapping(VamsasAppDatastore datastore,...
78		jalview.datamodel.Mapping mjvmapping,
79		uk.ac.vamsas.objects.core.SequenceType from,
80		uk.ac.vamsas.objects.core.DataSet ds)
81		{
82	0	super(datastore, mjvmapping.getMap(), SequenceMapping.class);
83	0	this.from = from;
84	0	this.ds = ds;
85	0	this.mjvmapping = mjvmapping;
86	0	validate();
87	0	doSync();
88		}
89
90		/**
91		* local check that extant mapping context is valid
92		*/
		0% Uncovered Elements: 13 (13) Complexity: 7 Complexity Density: 1
93	0	public void validate()...
94		{
95
96	0	SequenceMapping sequenceMapping = (SequenceMapping) vobj;
97	0	if (sequenceMapping == null)
98		{
99	0	return;
100		}
101	0	if (from != null && sequenceMapping.getLoc() != from)
102		{
103	0	Console.warn("Probable IMPLEMENTATION ERROR: " + from
104		+ " doesn't match the local mapping sequence.");
105		}
106	0	if (ds != null && sequenceMapping.is__stored_in_document()
107		&& sequenceMapping.getV_parent() != ds)
108		{
109	0	Console.warn("Probable IMPLEMENTATION ERROR: " + ds
110		+ " doesn't match the parent of the bound sequence mapping object.");
111		}
112		}
113
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
114	0	public void addToDocument()...
115		{
116	0	add(mjvmapping, from, ds);
117		}
118
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
119	0	public void addFromDocument()...
120		{
121	0	add((SequenceMapping) vobj);
122		}
123
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
124	0	public void conflict()...
125		{
126	0	conflict(mjvmapping, (SequenceMapping) vobj);
127
128		}
129
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
130	0	public void updateToDoc()...
131		{
132	0	update(mjvmapping, (SequenceMapping) vobj);
133		}
134
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
135	0	public void updateFromDoc()...
136		{
137	0	update((SequenceMapping) vobj, (jalview.datamodel.Mapping) jvobj);
138		}
139
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
140	0	private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)...
141		{
142	0	jalview.bin.Console.errPrintln("Conflict in update of sequenceMapping "
143		+ sequenceMapping.getVorbaId());
144		}
145
		0% Uncovered Elements: 50 (50) Complexity: 10 Complexity Density: 0.31
146	0	private void add(Mapping mjvmapping,...
147		uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)
148		{
149	0	SequenceI jvto = mjvmapping.getTo();
150	0	while (jvto.getDatasetSequence() != null)
151		{
152	0	jvto = jvto.getDatasetSequence();
153		}
154	0	SequenceType to = (SequenceType) getjv2vObj(jvto);
155	0	if (to == null)
156		{
157	0	Console.warn(
158		"FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
159	0	return;
160		}
161	0	SequenceMapping sequenceMapping = new SequenceMapping();
162	0	sequenceMapping.setLoc(from);
163	0	sequenceMapping.setMap(to);
164	0	boolean dnaToProt = false, sense = false;
165		// ensure that we create a mapping with the correct sense
166	0	if (((Sequence) sequenceMapping.getLoc()).getDictionary().equals(
167		uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
168		{
169	0	if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
170		uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
171		{
172	0	dnaToProt = true;
173	0	sense = true;
174		}
175		}
176		else
177		{
178	0	if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
179		uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
180		{
181	0	dnaToProt = true;
182	0	sense = false;
183		}
184		}
185
186	0	if (!dnaToProt)
187		{
188	0	Console.warn(
189		"Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
190	0	return;
191		}
192	0	if (ds == null)
193		{
194		// locate dataset for storage of SequenceMapping
195	0	if (sense)
196		{
197	0	ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
198		.getLoc()).getV_parent();
199		}
200		else
201		{
202	0	ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
203		.getMap()).getV_parent();
204		}
205		}
206	0	if (sense)
207		{
208	0	this.initMapType(sequenceMapping, mjvmapping.getMap(), true);
209		}
210		else
211		{
212	0	this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(),
213		true);
214		}
215	0	ds.addSequenceMapping(sequenceMapping);
216	0	sequenceMapping.setProvenance(
217		this.dummyProvenance("user defined coding region translation")); // TODO:
218		// correctly
219		// construct
220		// provenance
221		// based
222		// on
223		// source
224		// of
225		// mapping
226	0	bindjvvobj(mjvmapping.getMap(), sequenceMapping);
227
228	0	Console.debug(
229		"Successfully created mapping " + sequenceMapping.getVorbaId());
230		}
231
232		// private void update(jalview.util.MapList mjvmapping,
233		// SequenceMapping sequenceMapping)
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
234	0	{...
235	0	Console.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
236		}
237
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
238	0	private void update(SequenceMapping sequenceMapping,...
239		jalview.datamodel.Mapping mjvmapping)
240		{
241	0	Console.error("Not implemented: Update DBRef Mapping from Jalview");
242		}
243
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
244	0	private void update(jalview.datamodel.Mapping mjvmapping,...
245		SequenceMapping sequenceMapping)
246		{
247	0	Console.error("Not implemented: Jalview Update Sequence DBRef Mapping");
248		}
249
250		/**
251		* bind a SequenceMapping to a live AlCodonFrame element limitations:
252		* Currently, jalview only deals with mappings between dataset sequences, and
253		* even then, only between those that map from DNA to Protein.
254		*
255		* @param sequenceMapping
256		*/
		0% Uncovered Elements: 74 (74) Complexity: 17 Complexity Density: 0.35
257	0	private void add(SequenceMapping sequenceMapping)...
258		{
259	0	Object mobj;
260	0	SequenceI from = null, to = null;
261	0	boolean dnaToProt = false, sense = false;
262	0	Sequence sdloc = null, sdmap = null;
263	0	if (sequenceMapping.getLoc() instanceof AlignmentSequence)
264		{
265	0	sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc())
266		.getRefid();
267		}
268		else
269		{
270	0	sdloc = ((Sequence) sequenceMapping.getLoc());
271		}
272	0	if (sequenceMapping.getMap() instanceof AlignmentSequence)
273		{
274	0	sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap())
275		.getRefid();
276		}
277		else
278		{
279	0	sdmap = ((Sequence) sequenceMapping.getMap());
280		}
281	0	if (sdloc == null || sdmap == null)
282		{
283	0	Console.info("Ignoring non sequence-sequence mapping");
284	0	return;
285		}
286	0	mobj = this.getvObj2jv(sdloc);
287	0	if (mobj instanceof SequenceI)
288		{
289	0	from = (SequenceI) mobj;
290		}
291	0	mobj = this.getvObj2jv(sdmap);
292	0	if (mobj instanceof SequenceI)
293		{
294	0	to = (SequenceI) mobj;
295		}
296	0	if (from == null || to == null)
297		{
298
299	0	Console.error(
300		"Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
301	0	return;
302		}
303
304	0	if (sdloc.getDictionary().equals(
305		uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
306		{
307	0	if (sdmap.getDictionary().equals(
308		uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
309		{
310	0	dnaToProt = true;
311	0	sense = true;
312		}
313		// else {
314
315		// }
316		}
317		else
318		{
319	0	if (sdmap.getDictionary().equals(
320		uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
321		{
322	0	dnaToProt = true;
323	0	sense = false;
324		}
325		}
326		// create mapping storage object and make each dataset alignment reference
327		// it.
328	0	AlignmentI dsLoc = (AlignmentI) getvObj2jv(sdloc.getV_parent());
329	0	AlignmentI dsMap = (AlignmentI) getvObj2jv(sdmap.getV_parent());
330	0	AlignedCodonFrame acf = new AlignedCodonFrame();
331
332	0	if (dsLoc != null && dsLoc != dsMap)
333		{
334	0	dsLoc.addCodonFrame(acf);
335		}
336	0	if (dsMap != null)
337		{
338	0	dsMap.addCodonFrame(acf);
339		}
340		// create and add the new mapping to (each) dataset's codonFrame
341
342	0	jalview.util.MapList mapping = null;
343	0	if (dnaToProt)
344		{
345	0	if (!sense)
346		{
347	0	mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
348	0	mapping = new jalview.util.MapList(mapping.getToRanges(),
349		mapping.getFromRanges(), mapping.getToRatio(),
350		mapping.getFromRatio());
351	0	acf.addMap(to, from, mapping);
352		}
353		else
354		{
355	0	mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
356	0	acf.addMap(from, to, mapping);
357		}
358		}
359		else
360		{
361	0	mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense
362	0	acf.addMap(from, to, mapping);
363		}
364	0	bindjvvobj(mapping, sequenceMapping);
365	0	jalview.structure.StructureSelectionManager
366		.getStructureSelectionManager(Desktop.instance)
367		.registerMapping(acf);
368		// Try to link up any conjugate database references in the two sequences
369		// matchConjugateDBRefs(from, to, mapping);
370		// Try to propagate any dbrefs across this mapping.
371
372		}
373
374		/**
375		* Complete any 'to' references in jalview.datamodel.Mapping objects
376		* associated with conjugate DBRefEntry under given mapping
377		*
378		* @param from
379		* sequence corresponding to from reference for sequence mapping
380		* @param to
381		* sequence correspondeing to to reference for sequence mapping
382		* @param smap
383		* maplist parsed in same sense as from and to
384		*/
		0% Uncovered Elements: 59 (59) Complexity: 20 Complexity Density: 0.65
385	0	private void matchConjugateDBRefs(SequenceI from, SequenceI to,...
386		jalview.util.MapList smap)
387		{
388	0	if (from.getDBRefs() == null && to.getDBRefs() == null)
389		{
390	0	if (Console.isDebugEnabled())
391		{
392	0	Console.debug("Not matching conjugate refs for " + from.getName()
393		+ " and " + to.getName());
394		}
395	0	return;
396		}
397	0	if (Console.isDebugEnabled())
398		{
399	0	Console.debug("Matching conjugate refs for " + from.getName()
400		+ " and " + to.getName());
401		}
402	0	List<DBRefEntry> fdb = from.getDBRefs();
403	0	List<DBRefEntry> tdb = new ArrayList<DBRefEntry>(to.getDBRefs());
404	0	int tdblen = to.getDBRefs().size();
405		//
406		//
407		// YOWSER
408		//
409		// System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
410		//
411		//
412		//
413		//
414	0	Vector matched = new Vector();
415	0	jalview.util.MapList smapI = smap.getInverse();
416	0	for (int f = 0, fn = fdb.size(); f < fn; f++)
417		{
418	0	jalview.datamodel.DBRefEntry fe = fdb.get(f);
419	0	jalview.datamodel.Mapping fmp = fe.getMap();
420	0	boolean fmpnnl = (fmp != null);
421		// if (fmpnnl && fmp.getTo()!=null)
422		// {
423		// Cache.debug("Not overwriting existing To reference in
424		// "+fe);
425		// continue;
426		// }
427		// smap from maps from fe.local to fe.map
428	0	boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap())
429		: false;
430		// smap from maps from fe.map to fe.local.
431	0	boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap())
432		: false;
433	0	for (int t = 0; t < tdblen; t++)
434		{
435	0	jalview.datamodel.DBRefEntry te = tdb.get(t);
436	0	if (te != null)
437		{
438	0	if (fe.getSource().equals(te.getSource())
439		&& fe.getAccessionId().equals(te.getAccessionId()))
440		{
441	0	jalview.datamodel.Mapping tmp = te.getMap();
442	0	boolean tmpnnl = tmp != null;
443	0	if (tmpnnl && tmp.getTo() != null)
444		{
445
446		}
447		// smap to maps from te.local to te.map
448	0	boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap())
449		: false;
450		// smap to maps from te.map to te.local
451	0	boolean smaptotemap2local = (tmpnnl)
452		? smapI.equals(fmp.getMap())
453		: false;
454	0	if (smapfromlocal2fe && smaptotemap2local)
455		{
456		// smap implies mapping from to to from
457	0	fmp.setTo(to);
458	0	tmp.setTo(from);
459		}
460	0	else if (smapfromfemap2local && smaptolocal2tm)
461		{
462	0	fmp.setTo(to);
463		}
464		}
465
466		}
467		}
468		}
469		}
470		}