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StructureChooserQuerySource | 51 | 46 | 25 |
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.gui.structurechooser; | |
22 | ||
23 | import java.util.Locale; | |
24 | ||
25 | import java.util.Collection; | |
26 | import java.util.List; | |
27 | import java.util.Objects; | |
28 | import java.util.Vector; | |
29 | ||
30 | import javax.swing.JTable; | |
31 | import javax.swing.table.TableModel; | |
32 | ||
33 | import jalview.datamodel.DBRefEntry; | |
34 | import jalview.datamodel.PDBEntry; | |
35 | import jalview.datamodel.SequenceI; | |
36 | import jalview.fts.api.FTSData; | |
37 | import jalview.fts.api.FTSDataColumnI; | |
38 | import jalview.fts.api.FTSRestClientI; | |
39 | import jalview.fts.core.FTSDataColumnPreferences; | |
40 | import jalview.fts.core.FTSRestRequest; | |
41 | import jalview.fts.core.FTSRestResponse; | |
42 | import jalview.jbgui.FilterOption; | |
43 | ||
44 | /** | |
45 | * logic for querying sources of structural data for structures of sequences | |
46 | * | |
47 | * @author jprocter | |
48 | * | |
49 | * @param <T> | |
50 | */ | |
51 | public abstract class StructureChooserQuerySource | |
52 | { | |
53 | ||
54 | protected FTSDataColumnPreferences docFieldPrefs; | |
55 | ||
56 | /** | |
57 | * max length of a GET URL (probably :( ) | |
58 | */ | |
59 | protected static int MAX_QLENGTH = 7820; | |
60 | ||
61 | 138 | public StructureChooserQuerySource() |
62 | { | |
63 | } | |
64 | ||
65 | 0 | public static StructureChooserQuerySource getPDBfts() |
66 | { | |
67 | 0 | return new PDBStructureChooserQuerySource(); |
68 | } | |
69 | ||
70 | 0 | public static StructureChooserQuerySource getTDBfts() |
71 | { | |
72 | 0 | return new ThreeDBStructureChooserQuerySource(); |
73 | } | |
74 | ||
75 | 107 | public FTSDataColumnPreferences getDocFieldPrefs() |
76 | { | |
77 | 107 | return docFieldPrefs; |
78 | } | |
79 | ||
80 | 0 | public void setDocFieldPrefs(FTSDataColumnPreferences docFieldPrefs) |
81 | { | |
82 | 0 | this.docFieldPrefs = docFieldPrefs; |
83 | } | |
84 | ||
85 | 0 | public FTSDataColumnPreferences getInitialFieldPreferences() |
86 | { | |
87 | 0 | return docFieldPrefs; |
88 | } | |
89 | ||
90 | /** | |
91 | * Builds a query string for a given sequences using its DBRef entries | |
92 | * | |
93 | * @param seq | |
94 | * the sequences to build a query for | |
95 | * @return the built query string | |
96 | */ | |
97 | ||
98 | public abstract String buildQuery(SequenceI seq); | |
99 | ||
100 | /** | |
101 | * Remove the following special characters from input string +, -, &, !, (, ), | |
102 | * {, }, [, ], ^, ", ~, *, ?, :, \ | |
103 | * | |
104 | * @param seqName | |
105 | * @return | |
106 | */ | |
107 | 0 | public static String sanitizeSeqName(String seqName) |
108 | { | |
109 | 0 | Objects.requireNonNull(seqName); |
110 | 0 | return seqName.replaceAll("\\[\\d*\\]", "") |
111 | .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+"); | |
112 | } | |
113 | ||
114 | /** | |
115 | * Ensures sequence ref names are not less than 3 characters and does not | |
116 | * contain a database name | |
117 | * | |
118 | * @param seqName | |
119 | * @return | |
120 | */ | |
121 | 0 | static boolean isValidSeqName(String seqName) |
122 | { | |
123 | // jalview.bin.Console.outPrintln("seqName : " + seqName); | |
124 | 0 | String ignoreList = "pdb,uniprot,swiss-prot"; |
125 | 0 | if (seqName.length() < 3) |
126 | { | |
127 | 0 | return false; |
128 | } | |
129 | 0 | if (seqName.contains(":")) |
130 | { | |
131 | 0 | return false; |
132 | } | |
133 | 0 | seqName = seqName.toLowerCase(Locale.ROOT); |
134 | 0 | for (String ignoredEntry : ignoreList.split(",")) |
135 | { | |
136 | 0 | if (seqName.contains(ignoredEntry)) |
137 | { | |
138 | 0 | return false; |
139 | } | |
140 | } | |
141 | 0 | return true; |
142 | } | |
143 | ||
144 | 0 | static String getDBRefId(DBRefEntry dbRef) |
145 | { | |
146 | 0 | String ref = dbRef.getAccessionId().replaceAll("GO:", ""); |
147 | 0 | return ref; |
148 | } | |
149 | ||
150 | 0 | static PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries) |
151 | { | |
152 | 0 | Objects.requireNonNull(id); |
153 | 0 | Objects.requireNonNull(pdbEntries); |
154 | 0 | PDBEntry foundEntry = null; |
155 | 0 | for (PDBEntry entry : pdbEntries) |
156 | { | |
157 | 0 | if (entry.getId().equalsIgnoreCase(id)) |
158 | { | |
159 | 0 | return entry; |
160 | } | |
161 | } | |
162 | 0 | return foundEntry; |
163 | } | |
164 | ||
165 | /** | |
166 | * FTSRestClient specific query builder to recover associated structure data | |
167 | * records for a sequence | |
168 | * | |
169 | * @param seq | |
170 | * - seq to generate a query for | |
171 | * @param wantedFields | |
172 | * - fields to retrieve | |
173 | * @param selectedFilterOpt | |
174 | * - criterion for ranking results (e.g. resolution) | |
175 | * @param b | |
176 | * - sort ascending or descending | |
177 | * @return | |
178 | * @throws Exception | |
179 | */ | |
180 | public abstract FTSRestResponse fetchStructuresMetaData(SequenceI seq, | |
181 | Collection<FTSDataColumnI> wantedFields, | |
182 | FilterOption selectedFilterOpt, boolean b) throws Exception; | |
183 | ||
184 | /** | |
185 | * FTSRestClient specific query builder to pick top ranked entry from a | |
186 | * fetchStructuresMetaData query | |
187 | * | |
188 | * @param seq | |
189 | * - seq to generate a query for | |
190 | * @param discoveredStructuresSet | |
191 | * - existing set of entries - allows client side selection | |
192 | * @param wantedFields | |
193 | * - fields to retrieve | |
194 | * @param selectedFilterOpt | |
195 | * - criterion for ranking results (e.g. resolution) | |
196 | * @param b | |
197 | * - sort ascending or descending | |
198 | * @return | |
199 | * @throws Exception | |
200 | */ | |
201 | public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq, | |
202 | Collection<FTSData> discoveredStructuresSet, | |
203 | Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy, | |
204 | boolean b) throws Exception; | |
205 | ||
206 | /** | |
207 | * | |
208 | * @param discoveredStructuresSet | |
209 | * @return the table model for the given result set for this engine | |
210 | */ | |
211 | 3 | public TableModel getTableModel( |
212 | Collection<FTSData> discoveredStructuresSet) | |
213 | { | |
214 | 3 | return FTSRestResponse.getTableModel(getLastFTSRequest(), |
215 | discoveredStructuresSet); | |
216 | } | |
217 | ||
218 | protected abstract FTSRestRequest getLastFTSRequest(); | |
219 | ||
220 | public abstract PDBEntry[] collectSelectedRows(JTable restable, | |
221 | int[] selectedRows, List<SequenceI> selectedSeqsToView); | |
222 | ||
223 | /** | |
224 | * @param VIEWS_FILTER | |
225 | * - a String key that can be used by the caller to tag the returned | |
226 | * filter options to distinguish them in a collection | |
227 | * @return list of FilterOption - convention is that the last one in the list | |
228 | * will be constructed with 'addSeparator==true' | |
229 | */ | |
230 | public abstract List<FilterOption> getAvailableFilterOptions( | |
231 | String VIEWS_FILTER); | |
232 | ||
233 | /** | |
234 | * construct a structure chooser query source for the given set of sequences | |
235 | * | |
236 | * @param selectedSeqs | |
237 | * @return PDBe or 3DB query source | |
238 | */ | |
239 | 65 | public static StructureChooserQuerySource getQuerySourceFor( |
240 | SequenceI[] selectedSeqs) | |
241 | { | |
242 | 65 | ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource(); |
243 | 65 | boolean hasUniprot = false, hasCanonical = false; |
244 | 65 | boolean hasNA = false, hasProtein = false; |
245 | 65 | int protWithoutUni = 0; |
246 | 65 | int protWithoutCanon = 0; |
247 | 65 | for (SequenceI seq : selectedSeqs) |
248 | { | |
249 | 65 | hasNA |= !seq.isProtein(); |
250 | 65 | hasProtein |= seq.isProtein(); |
251 | 65 | if (seq.isProtein()) |
252 | { | |
253 | 65 | int refsAvailable = ThreeDBStructureChooserQuerySource |
254 | .checkUniprotRefs(seq.getDBRefs()); | |
255 | 65 | if (refsAvailable > -2) |
256 | { | |
257 | 10 | if (refsAvailable > -1) |
258 | { | |
259 | 8 | hasCanonical = true; |
260 | } | |
261 | else | |
262 | { | |
263 | 2 | protWithoutCanon++; |
264 | } | |
265 | 10 | hasUniprot = true; |
266 | } | |
267 | else | |
268 | { | |
269 | 55 | protWithoutUni++; |
270 | ||
271 | } | |
272 | } | |
273 | } | |
274 | // | |
275 | // logic: all canonicals - no fetchdb | |
276 | // some uniprot no canonicals: defer to PDB, user can optionally fetch | |
277 | // | |
278 | 65 | if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0 |
279 | && protWithoutUni == 0) | |
280 | ||
281 | { | |
282 | 8 | return tdbSource; |
283 | } | |
284 | 57 | return new PDBStructureChooserQuerySource(); |
285 | } | |
286 | ||
287 | /** | |
288 | * some filter options may mean the original query needs to be executed again. | |
289 | * | |
290 | * @param selectedFilterOpt | |
291 | * @return true if the fetchStructuresMetadata method needs to be called again | |
292 | */ | |
293 | public abstract boolean needsRefetch(FilterOption selectedFilterOpt); | |
294 | ||
295 | 4 | public void updateAvailableFilterOptions(String VIEWS_FILTER, |
296 | List<FilterOption> xtantOptions, Collection<FTSData> lastFTSData) | |
297 | { | |
298 | // TODO Auto-generated method stub | |
299 | ||
300 | } | |
301 | } |