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.StructureMapping;
25 import jalview.ws.sifts.MappingOutputPojo;
26 import jalview.ws.sifts.SiftsException;
27 import jalview.xml.binding.sifts.Entry.Entity;
29 import java.util.HashSet;
31 public interface SiftsClientI
34 * Get the DB Accession Id for the SIFTs Entry
38 public String getDbAccessionId();
41 * Get DB Coordinate system for the SIFTs Entry
45 public String getDbCoordSys();
48 * Get DB Evidence for the SIFTs Entry
52 public String getDbEvidence();
55 * Get DB Source for the SIFTs Entry
59 public String getDbSource();
62 * Get DB version for the SIFTs Entry
66 public String getDbVersion();
69 * Get Number of Entities available in the SIFTs Entry
73 public int getEntityCount();
76 * Get a unique Entity by its Id
79 * ID of the entity to fetch
83 public Entity getEntityById(String id) throws SiftsException;
86 * Get all accession Ids available in the current SIFTs entry
88 * @return a unique set of discovered accession strings
90 public HashSet<String> getAllMappingAccession();
93 * Check if the accessionId is available in current SIFTs Entry
98 public boolean isFoundInSiftsEntry(String accessionId);
101 * Get the standard DB referenced by the SIFTs Entry
105 public String[] getEntryDBs();
111 * @return Sequence<->Structure mapping as int[][]
113 public StringBuffer getMappingOutput(MappingOutputPojo mop);
118 * sequence to generate mapping against the structure
120 * PDB file for the mapping
122 * the chain of the entry to use for mapping
123 * @return StructureMapping
124 * @throws SiftsException
126 public StructureMapping getSiftsStructureMapping(SequenceI seq,
127 String pdbFile, String chain) throws SiftsException;
130 * Get residue by residue mapping for a given Sequence and SIFTs entity
133 * Id of the target entity in the SIFTs entry
136 * @return generated mapping
139 public int[][] getGreedyMapping(String entityId, SequenceI seq,
140 java.io.PrintStream os) throws SiftsException;