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.HashMap;
30 import java.util.HashSet;
32 public interface SiftsClientI
35 * Get the DB Accession Id for the SIFTs Entry
39 public String getDbAccessionId();
42 * Get DB Coordinate system for the SIFTs Entry
46 public String getDbCoordSys();
49 * Get DB Evidence for the SIFTs Entry
53 public String getDbEvidence();
56 * Get DB Source for the SIFTs Entry
60 public String getDbSource();
63 * Get DB version for the SIFTs Entry
67 public String getDbVersion();
70 * Get Number of Entities available in the SIFTs Entry
74 public int getEntityCount();
77 * Get a unique Entity by its Id
80 * ID of the entity to fetch
84 public Entity getEntityById(String id) throws SiftsException;
87 * Get all accession Ids available in the current SIFTs entry
89 * @return a unique set of discovered accession strings
91 public HashSet<String> getAllMappingAccession();
94 * Check if the accessionId is available in current SIFTs Entry
99 public boolean isAccessionMatched(String accessionId);
102 * Get the standard DB referenced by the SIFTs Entry
106 public String[] getEntryDBs();
112 * @return Sequence<->Structure mapping as int[][]
113 * @throws SiftsException
115 public StringBuffer getMappingOutput(MappingOutputPojo mop)
116 throws SiftsException;
121 * sequence to generate mapping against the structure
123 * PDB file for the mapping
125 * the chain of the entry to use for mapping
126 * @return StructureMapping
127 * @throws SiftsException
129 public StructureMapping getSiftsStructureMapping(SequenceI seq,
130 String pdbFile, String chain) throws SiftsException;
133 * Get residue by residue mapping for a given Sequence and SIFTs entity
136 * Id of the target entity in the SIFTs entry
139 * @return generated mapping
142 public HashMap<Integer, int[]> getGreedyMapping(String entityId,
144 java.io.PrintStream os) throws SiftsException;