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.
21 package jalview.gui.structurechooser;
23 import java.util.Locale;
25 import java.util.ArrayList;
26 import java.util.Arrays;
27 import java.util.BitSet;
28 import java.util.Collection;
29 import java.util.Collections;
30 import java.util.Comparator;
31 import java.util.List;
33 import jalview.datamodel.SequenceI;
34 import jalview.fts.api.FTSData;
35 import jalview.fts.core.FTSRestRequest;
37 public class TDBResultAnalyser
41 * model categories - update as needed. warnings output if unknown types
44 * Order denotes 'trust'
46 private static List<String> EXP_CATEGORIES = Arrays
48 { "EXPERIMENTALLY DETERMINED", "DEEP-LEARNING", "TEMPLATE-BASED",
49 "AB-INITIO", "CONFORMATIONAL ENSEMBLE" });
51 private SequenceI seq;
53 private Collection<FTSData> collectedResults;
55 private FTSRestRequest lastTdbRequest;
63 private int idx_mqual;
65 private int idx_resol;
70 private String filter = null;
73 * limit to particular source
75 private String sourceFilter = null;
77 private int idx_mprov;
79 public TDBResultAnalyser(SequenceI seq,
80 Collection<FTSData> collectedResults,
81 FTSRestRequest lastTdbRequest, String fieldToFilterBy,
85 this.collectedResults = collectedResults;
86 this.lastTdbRequest = lastTdbRequest;
87 this.filter = fieldToFilterBy;
88 this.sourceFilter = string;
89 idx_ups = lastTdbRequest.getFieldIndex("Uniprot Start");
90 idx_upe = lastTdbRequest.getFieldIndex("Uniprot End");
91 idx_mcat = lastTdbRequest.getFieldIndex("Model Category");
92 idx_mprov = lastTdbRequest.getFieldIndex("Provider");
93 idx_mqual = lastTdbRequest.getFieldIndex("Confidence");
94 idx_resol = lastTdbRequest.getFieldIndex("Resolution");
98 * maintain and resolve categories to 'trust order' TODO: change the trust
99 * scheme to something comprehensible.
102 * @return 0 for null cat, less than zero for others
104 public final int scoreCategory(String cat)
110 String upper_cat = cat.toUpperCase(Locale.ROOT);
111 int idx = EXP_CATEGORIES.indexOf(upper_cat);
114 System.out.println("Unknown category: '" + cat + "'");
115 EXP_CATEGORIES.add(upper_cat);
116 idx = EXP_CATEGORIES.size() - 1;
118 return -EXP_CATEGORIES.size() - idx;
122 * sorts records discovered by 3D beacons and excludes any that don't
123 * intersect with the sequence's start/end rage
127 public List<FTSData> getFilteredResponse()
129 List<FTSData> filteredResponse = new ArrayList<FTSData>();
131 // ignore anything outside the sequence region
132 for (FTSData row : collectedResults)
134 if (row.getSummaryData() != null
135 && row.getSummaryData()[idx_ups] != null)
137 int up_s = (Integer) row.getSummaryData()[idx_ups];
138 int up_e = (Integer) row.getSummaryData()[idx_upe];
139 String provider = (String) row.getSummaryData()[idx_mprov];
140 String mcat = (String) row.getSummaryData()[idx_mcat];
141 // this makes sure all new categories are in the score array.
142 int scorecat = scoreCategory(mcat);
143 if (sourceFilter == null || sourceFilter.equals(provider))
145 if (seq == row.getSummaryData()[0] && up_e > seq.getStart()
146 && up_s < seq.getEnd())
148 filteredResponse.add(row);
153 // sort according to decreasing length,
155 Collections.sort(filteredResponse, new Comparator<FTSData>()
158 public int compare(FTSData o1, FTSData o2)
160 Object[] o1data = o1.getSummaryData();
161 Object[] o2data = o2.getSummaryData();
162 int o1_s = (Integer) o1data[idx_ups];
163 int o1_e = (Integer) o1data[idx_upe];
164 int o1_cat = scoreCategory((String) o1data[idx_mcat]);
165 String o1_prov = ((String) o1data[idx_mprov])
166 .toUpperCase(Locale.ROOT);
167 int o2_s = (Integer) o2data[idx_ups];
168 int o2_e = (Integer) o2data[idx_upe];
169 int o2_cat = scoreCategory((String) o2data[idx_mcat]);
170 String o2_prov = ((String) o2data[idx_mprov])
171 .toUpperCase(Locale.ROOT);
173 if (o1_cat == o2_cat)
177 int o1_xtent = o1_e - o1_s;
178 int o2_xtent = o2_e - o2_s;
179 if (o1_xtent == o2_xtent)
181 if (o1_cat == scoreCategory(EXP_CATEGORIES.get(0)))
183 if (o1_prov.equals(o2_prov))
185 if ("PDBE".equals(o1_prov))
187 if (eitherNull(idx_resol, o1data, o2data))
189 return nonNullFirst(idx_resol, o1data, o2data);
191 // experimental structures, so rank on quality
192 double o1_res = (Double) o1data[idx_resol];
193 double o2_res = (Double) o2data[idx_resol];
194 return (o2_res < o1_res) ? 1
195 : (o2_res == o1_res) ? 0 : -1;
199 return 0; // no change in order
204 // PDBe always ranked above all other experimentally
205 // determined categories
206 return "PDBE".equals(o1_prov) ? -1
207 : "PDBE".equals(o2_prov) ? 1 : 0;
212 if (eitherNull(idx_mqual, o1data, o2data))
214 return nonNullFirst(idx_mqual, o1data, o2data);
216 // models, so rank on qmean - b
217 double o1_mq = (Double) o1data[idx_mqual];
218 double o2_mq = (Double) o2data[idx_mqual];
219 return (o2_mq < o1_mq) ? 1 : (o2_mq == o1_mq) ? 0 : -1;
224 return o1_xtent - o2_xtent;
234 return o2_cat - o1_cat;
238 private int nonNullFirst(int idx_resol, Object[] o1data,
241 return o1data[idx_resol] == o2data[idx_resol] ? 0
242 : o1data[idx_resol] != null ? -1 : 1;
245 private boolean eitherNull(int idx_resol, Object[] o1data,
248 return (o1data[idx_resol] == null || o2data[idx_resol] == null);
252 public boolean equals(Object obj)
254 return super.equals(obj);
257 return filteredResponse;
261 * return list of structures to be marked as selected for this sequence
262 * according to given criteria
264 * @param filteredStructures
265 * - sorted, filtered structures from getFilteredResponse
268 public List<FTSData> selectStructures(List<FTSData> filteredStructures)
270 List<FTSData> selected = new ArrayList<FTSData>();
271 BitSet cover = new BitSet();
272 cover.set(seq.getStart(), seq.getEnd());
273 // walk down the list of structures, selecting some to add to selected
274 // TODO: could do simple DP - double loop to select largest number of
275 // structures covering largest number of sites
276 for (FTSData structure : filteredStructures)
278 Object[] odata = structure.getSummaryData();
279 int o1_s = (Integer) odata[idx_ups];
280 int o1_e = (Integer) odata[idx_upe];
281 int o1_cat = scoreCategory((String) odata[idx_mcat]);
282 BitSet scover = new BitSet();
283 // measure intersection
284 scover.set(o1_s, o1_e);
286 if (scover.cardinality() > 4)
288 selected.add(structure);
289 // clear the range covered by this structure
290 cover.andNot(scover);
293 if (selected.size() == 0)
297 // final step is to sort on length - this might help the superposition
299 Collections.sort(selected, new Comparator<FTSData>()
302 public int compare(FTSData o1, FTSData o2)
304 Object[] o1data = o1.getSummaryData();
305 Object[] o2data = o2.getSummaryData();
306 int o1_xt = ((Integer) o1data[idx_upe])
307 - ((Integer) o1data[idx_ups]);
308 int o1_cat = scoreCategory((String) o1data[idx_mcat]);
309 int o2_xt = ((Integer) o2data[idx_upe] - (Integer) o2data[idx_ups]);
310 int o2_cat = scoreCategory((String) o2data[idx_mcat]);
311 return o2_xt - o1_xt;
315 ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE))
317 return selected.subList(0, 1);