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.xml.binding.sifts.Entry.Entity;
27 import java.util.HashSet;
29 public interface SiftsClientI
32 * Get the DB Accession Id for the SIFTs Entry
36 public String getDbAccessionId();
39 * Get DB Coordinate system for the SIFTs Entry
43 public String getDbCoordSys();
46 * Get DB Evidence for the SIFTs Entry
50 public String getDbEvidence();
53 * Get DB Source for the SIFTs Entry
57 public String getDbSource();
60 * Get DB version for the SIFTs Entry
64 public String getDbVersion();
67 * Get Number of Entities available in the SIFTs Entry
71 public int getEntityCount();
74 * Get a unique Entity by its Id
77 * ID of the entity to fetch
81 public Entity getEntityById(String id) throws Exception;
84 * Get all accession Ids available in the current SIFTs entry
86 * @return a unique set of discovered accession strings
88 public HashSet<String> getAllMappingAccession();
91 * Check if the accessionId is available in current SIFTs Entry
96 public boolean isFoundInSiftsEntry(String accessionId);
99 * Get the standard DB referenced by the SIFTs Entry
103 public String[] getEntryDBs();
106 * Get the SIFTs Entry details
108 public void getEntryDetails();
119 * structure sequence id
121 * type of sequence for the mapping (pep or protein)
123 * @return sequence->structure mapping as int [][]
125 public StringBuffer getMappingOutput(String seq1, String seq2,
126 String seqID1, String seqID2, String seqType, int nochunks);
131 * sequence to generate mapping against the structure
133 * PDB file for the mapping
135 * the chain of the entry to use for mapping
136 * @return StructureMapping
138 public StructureMapping getSiftsStructureMapping(SequenceI seq, String pdbFile,
142 * Get residue by residue mapping for a given Sequence and SIFTs entity
145 * Id of the target entity in the SIFTs entry
148 * @return generated mapping
151 public int[][] getGreedyMapping(String entityId, SequenceI seq,
152 java.io.PrintStream os) throws Exception;