Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ContactMapHolder	31	31	16	0.00%	Show methods

Class ContactMapHolder

Class ContactMapHolder	Line # 31	Total Statements 31	Complexity 16	TOTAL Coverage 0.00%
getContactMaps() : Collection<ContactMatrixI>   getContactMaps() : Collection<ContactMatrixI>	3636	3.03	3.03	0.0 0.00%
getContactListFor(AlignmentAnnotation,int) : ContactListI   getContactListFor(AlignmentAnnotation,int) : ContactListI	4848	7.07	4.04	0.0 0.00%
addContactList(ContactMatrixI) : AlignmentAnnotation   addContactList(ContactMatrixI) : AlignmentAnnotation	7070	10.010	2.02	0.0 0.00%
getContactMatrixFor(AlignmentAnnotation) : ContactMatrixI   getContactMatrixFor(AlignmentAnnotation) : ContactMatrixI	9292	1.01	2.02	0.0 0.00%
addContactListFor(AlignmentAnnotation,ContactMatrixI) : void   addContactListFor(AlignmentAnnotation,ContactMatrixI) : void	9898	10.010	5.05	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.datamodel;
22
23		import java.util.Collection;
24		import java.util.Collections;
25		import java.util.HashMap;
26		import java.util.HashSet;
27		import java.util.Map;
28
29		import jalview.ws.datamodel.MappableContactMatrixI;
30
		0% Uncovered Elements: 52 (52) Complexity: 16 Complexity Density: 0.52
31		public class ContactMapHolder implements ContactMapHolderI
32		{
33
34		Map<Object, ContactMatrixI> contactmaps = new HashMap<>();
35
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
36	0	@Override...
37		public Collection<ContactMatrixI> getContactMaps()
38		{
39	0	if (contactmaps != null && contactmaps.size() > 0)
40		{
41		// defensive copy, and return non redundant set of ContactMatrixI
42		// instances
43	0	return new HashSet<ContactMatrixI>(contactmaps.values());
44		}
45	0	return Collections.EMPTY_LIST;
46		}
47
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.57
48	0	@Override...
49		public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
50		{
51	0	ContactMatrixI cm = contactmaps.get(_aa.annotationId);
52	0	if (cm == null)
53		{
54	0	return null;
55		}
56	0	if (cm instanceof MappableContactMatrixI)
57		{
58	0	if (_aa.sequenceRef != null)
59		{
60	0	return ((MappableContactMatrixI) cm)
61		.getMappableContactList(_aa.sequenceRef, column);
62		}
63		}
64		// TODO: could resolve sequence position to column position here
65		// TODO: what about for complexes - where contactMatrix may involve two or
66		// more sequences
67	0	return cm.getContactList(column);
68		}
69
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
70	0	@Override...
71		public AlignmentAnnotation addContactList(ContactMatrixI cm)
72		{
73
74	0	AlignmentAnnotation aa = new AlignmentAnnotation(cm.getAnnotLabel(),
75		cm.getAnnotDescr(), new Annotation[0]);
76	0	aa.graph = AlignmentAnnotation.CONTACT_MAP;
77	0	aa.graphMin = cm.getMin();
78	0	aa.graphMax = cm.getMax();
79	0	aa.editable = false;
80	0	aa.calcId = cm.getType();
81
82	0	contactmaps.put(aa.annotationId, cm);
83		// TODO: contact matrices could be intra or inter - more than one refseq
84		// possible!
85	0	if (cm instanceof MappableContactMatrixI)
86		{
87	0	aa.setSequenceRef(((MappableContactMatrixI) cm).getReferenceSeq());
88		}
89	0	return aa;
90		}
91
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
92	0	@Override...
93		public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann)
94		{
95	0	return contactmaps == null ? null : contactmaps.get(ann.annotationId);
96		}
97
		0% Uncovered Elements: 14 (14) Complexity: 5 Complexity Density: 0.5
98	0	@Override...
99		public void addContactListFor(AlignmentAnnotation annotation,
100		ContactMatrixI cm)
101		{
102		// update annotation with data from contact map
103	0	annotation.graphMin = cm.getMin();
104	0	annotation.graphMax = cm.getMax();
105	0	annotation.editable = false;
106	0	annotation.graph = AlignmentAnnotation.CONTACT_MAP;
107	0	annotation.calcId = cm.getType();
108	0	if (annotation.label == null || "".equals(annotation.label))
109		{
110	0	annotation.label = cm.getAnnotLabel();
111
112		}
113	0	if (annotation.description == null || "".equals(annotation.description))
114		{
115	0	annotation.description = cm.getAnnotDescr();
116		}
117	0	contactmaps.put(annotation.annotationId, cm);
118		}
119		}