Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SiftsClientI	34	0	0	-1.0 -	Show methods

Class SiftsClientI

Class SiftsClientI	Line # 34	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.SequenceI;
24		import jalview.structure.StructureMapping;
25		import jalview.ws.sifts.MappingOutputPojo;
26		import jalview.ws.sifts.SiftsException;
27		import jalview.xml.binding.sifts.Entry.Entity;
28
29		import java.util.HashMap;
30		import java.util.HashSet;
31
32		// JBPComment: this isn't a top-level Jalview API - should be in its own package api
33
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
34		public interface SiftsClientI
35		{
36		/**
37		* Get the DB Accession Id for the SIFTs Entry
38		*
39		* @return
40		*/
41		public String getDbAccessionId();
42
43		/**
44		* Get DB Coordinate system for the SIFTs Entry
45		*
46		* @return
47		*/
48		public String getDbCoordSys();
49
50		/**
51		* Get DB Source for the SIFTs Entry
52		*
53		* @return
54		*/
55		public String getDbSource();
56
57		/**
58		* Get DB version for the SIFTs Entry
59		*
60		* @return
61		*/
62		public String getDbVersion();
63
64		/**
65		* Get Number of Entities available in the SIFTs Entry
66		*
67		* @return
68		*/
69		public int getEntityCount();
70
71		/**
72		* Get a unique Entity by its Id
73		*
74		* @param id
75		* ID of the entity to fetch
76		* @return Entity
77		* @throws Exception
78		*/
79		public Entity getEntityById(String id) throws SiftsException;
80
81		/**
82		* Get all accession Ids available in the current SIFTs entry
83		*
84		* @return a unique set of discovered accession strings
85		*/
86		public HashSet<String> getAllMappingAccession();
87
88		/**
89		* Check if the accessionId is available in current SIFTs Entry
90		*
91		* @param accessionId
92		* @return
93		*/
94		public boolean isAccessionMatched(String accessionId);
95
96		/**
97		*
98		* @param mop
99		* MappingOutputPojo
100		* @return Sequence<->Structure mapping as int[][]
101		* @throws SiftsException
102		*/
103		public StringBuilder getMappingOutput(MappingOutputPojo mop)
104		throws SiftsException;
105
106		/**
107		*
108		* @param seq
109		* sequence to generate mapping against the structure
110		* @param pdbFile
111		* PDB file for the mapping
112		* @param chain
113		* the chain of the entry to use for mapping
114		* @return StructureMapping
115		* @throws SiftsException
116		*/
117		public StructureMapping getSiftsStructureMapping(SequenceI seq,
118		String pdbFile, String chain) throws SiftsException;
119
120		/**
121		* Get residue by residue mapping for a given Sequence and SIFTs entity
122		*
123		* @param entityId
124		* Id of the target entity in the SIFTs entry
125		* @param seq
126		* SequenceI
127		* @return generated mapping
128		* @throws Exception
129		*/
130		public HashMap<Integer, int[]> getGreedyMapping(String entityId,
131		SequenceI seq, java.io.PrintStream os) throws SiftsException;
132		}