2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import jalview.datamodel.SequenceI;
24 import jalview.structure.StructureMappingClient.StructureMappingException;
25 import jalview.ws.sifts.SiftsException;
26 import jalview.xml.binding.sifts.Entry.Entity;
28 import java.util.HashMap;
29 import java.util.HashSet;
31 // JBPComment: this isn't a top-level Jalview API - should be in its own package api
33 public interface SiftsClientI
36 * Get the DB Accession Id for the SIFTs Entry
40 public String getDbAccessionId();
43 * Get DB Coordinate system for the SIFTs Entry
47 public String getDbCoordSys();
50 * Get DB Source for the SIFTs Entry
54 public String getDbSource();
57 * Get DB version for the SIFTs Entry
61 public String getDbVersion();
64 * Get Number of Entities available in the SIFTs Entry
68 public int getEntityCount();
71 * Get a unique Entity by its Id
74 * ID of the entity to fetch
78 public Entity getEntityById(String id) throws SiftsException;
81 * Get all accession Ids available in the current SIFTs entry
83 * @return a unique set of discovered accession strings
85 public HashSet<String> getAllMappingAccession();
88 * Check if the accessionId is available in current SIFTs Entry
93 public boolean isAccessionMatched(String accessionId);
98 * Get residue by residue mapping for a given Sequence and SIFTs entity
101 * Id of the target entity in the SIFTs entry
104 * @return generated mapping
107 public HashMap<Integer, int[]> getGreedyMapping(String entityId,
108 SequenceI seq, java.io.PrintStream os) throws SiftsException,
109 StructureMappingException;