Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DBRefEntryI	27	0	0	-1.0 -	Show methods

Class DBRefEntryI

Class DBRefEntryI	Line # 27	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

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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.api;
22
23		import jalview.datamodel.Mapping;
24
25		//JBPComment: this is a datamodel API - so it should be in datamodel (it's a peer of SequenceI)
26
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
27		public interface DBRefEntryI
28		{
29		public boolean equalRef(DBRefEntryI entry);
30
31		/**
32		*
33		* @return Source DB name for this entry
34		*/
35		public String getSource();
36
37		/**
38		*
39		* @return Accession Id for this entry
40		*/
41		public String getAccessionId();
42
43		/**
44		*
45		* @param accessionId
46		* Accession Id for this entry
47		*/
48		public void setAccessionId(String accessionId);
49
50		/**
51		*
52		* @param source
53		* Source DB name for this entry
54		*/
55		public void setSource(String source);
56
57		/**
58		*
59		* @return Source DB version for this entry
60		*/
61		public String getVersion();
62
63		/**
64		*
65		* @param version
66		* Source DB version for this entry
67		*/
68		public void setVersion(String version);
69
70		/**
71		* access a mapping, if present that can be used to map positions from the
72		* associated dataset sequence to the DBRef's sequence frame.
73		*
74		* @return null or a valid mapping.
75		*/
76		public Mapping getMap();
77
78		/**
79		* Answers true if this object is either equivalent to, or can be 'improved'
80		* by, the given entry. Specifically, answers true if
81		* <ul>
82		* <li>source and accession are identical</li>
83		* <li>version is identical, or this version is of the format "someSource:0",
84		* in which case the version for the other entry replaces it</li>
85		* <li>mappings are not compared but if this entry has no mapping, replace
86		* with that for the other entry</li>
87		* </ul>
88		*
89		* @param otherEntry
90		* @return
91		*/
92		public boolean updateFrom(DBRefEntryI otherEntry);
93
94		/**
95		* Answers true if the ref looks like a primary (direct) database reference.
96		* <br>
97		* The only way a dbref's mappings can be fully verified is via the local
98		* sequence frame, so rather than use isPrimaryCandidate directly, please use
99		* SequenceI.getPrimaryDbRefs(). <br>
100		* Primary references indicate the local sequence data directly corresponds
101		* with the database record. All other references are secondary. Direct
102		* references indicate that part or all of the local sequence data can be
103		* mapped with another sequence, enabling annotation transfer.
104		* Cross-references indicate the local sequence data can be corresponded to
105		* some other linear coordinate system via a transformation. <br>
106		* This method is also sufficient to distinguish direct DBRefEntry mappings
107		* from other relationships - e.g. coding relationships (imply a 1:3/3:1
108		* mapping), but not transcript relationships, which imply a (possibly
109		* non-contiguous) 1:1 mapping.
110		*
111		* @return true if this reference provides a primary accession for the
112		* associated sequence object
113		*/
114		public boolean isPrimaryCandidate();
115
116		public boolean isCanonical();
117		}