1 package jalview.gui.structurechooser;
3 import java.util.ArrayList;
4 import java.util.Arrays;
5 import java.util.BitSet;
6 import java.util.Collection;
7 import java.util.Collections;
8 import java.util.Comparator;
11 import jalview.datamodel.SequenceI;
12 import jalview.fts.api.FTSData;
13 import jalview.fts.core.FTSRestRequest;
15 public class TDBResultAnalyser
19 * model categories - update as needed. warnings output if unknown types
22 * Order denotes 'trust'
24 private static List<String> EXP_CATEGORIES = Arrays
26 { "EXPERIMENTALLY DETERMINED", "DEEP-LEARNING", "TEMPLATE-BASED",
27 "AB-INITIO", "CONFORMATIONAL ENSEMBLE" });
29 private SequenceI seq;
31 private Collection<FTSData> collectedResults;
33 private FTSRestRequest lastTdbRequest;
41 private int idx_mqual;
43 private int idx_resol;
48 private String filter = null;
51 * limit to particular source
53 private String sourceFilter = null;
55 private int idx_mprov;
57 public TDBResultAnalyser(SequenceI seq,
58 Collection<FTSData> collectedResults,
59 FTSRestRequest lastTdbRequest, String fieldToFilterBy,
63 this.collectedResults = collectedResults;
64 this.lastTdbRequest = lastTdbRequest;
65 this.filter = fieldToFilterBy;
66 this.sourceFilter = string;
67 idx_ups = lastTdbRequest.getFieldIndex("Uniprot Start");
68 idx_upe = lastTdbRequest.getFieldIndex("Uniprot End");
69 idx_mcat = lastTdbRequest.getFieldIndex("Model Category");
70 idx_mprov = lastTdbRequest.getFieldIndex("Provider");
71 idx_mqual = lastTdbRequest.getFieldIndex("Confidence");
72 idx_resol = lastTdbRequest.getFieldIndex("Resolution");
76 * maintain and resolve categories to 'trust order' TODO: change the trust
77 * scheme to something comprehensible.
80 * @return 0 for null cat, less than zero for others
82 public final int scoreCategory(String cat)
88 String upper_cat = cat.toUpperCase();
89 int idx = EXP_CATEGORIES.indexOf(upper_cat);
92 System.out.println("Unknown category: '" + cat + "'");
93 EXP_CATEGORIES.add(upper_cat);
94 idx = EXP_CATEGORIES.size() - 1;
96 return -EXP_CATEGORIES.size() - idx;
100 * sorts records discovered by 3D beacons and excludes any that don't
101 * intersect with the sequence's start/end rage
105 public List<FTSData> getFilteredResponse()
107 List<FTSData> filteredResponse = new ArrayList<FTSData>();
109 // ignore anything outside the sequence region
110 for (FTSData row : collectedResults)
112 int up_s = (Integer) row.getSummaryData()[idx_ups];
113 int up_e = (Integer) row.getSummaryData()[idx_upe];
114 String provider = (String) row.getSummaryData()[idx_mprov];
115 String mcat = (String) row.getSummaryData()[idx_mcat];
116 // this makes sure all new categories are in the score array.
117 int scorecat = scoreCategory(mcat);
118 if (sourceFilter == null || sourceFilter.equals(provider))
120 if (seq == row.getSummaryData()[0] && up_e > seq.getStart()
121 && up_s < seq.getEnd())
123 filteredResponse.add(row);
127 // sort according to decreasing length,
129 Collections.sort(filteredResponse, new Comparator<FTSData>()
132 public int compare(FTSData o1, FTSData o2)
134 Object[] o1data = o1.getSummaryData();
135 Object[] o2data = o2.getSummaryData();
136 int o1_s = (Integer) o1data[idx_ups];
137 int o1_e = (Integer) o1data[idx_upe];
138 int o1_cat = scoreCategory((String) o1data[idx_mcat]);
139 String o1_prov= ((String) o1data[idx_mprov]).toUpperCase();
140 int o2_s = (Integer) o2data[idx_ups];
141 int o2_e = (Integer) o2data[idx_upe];
142 int o2_cat = scoreCategory((String) o2data[idx_mcat]);
143 String o2_prov= ((String) o2data[idx_mprov]).toUpperCase();
146 if (o1_cat == o2_cat)
150 int o1_xtent = o1_e - o1_s;
151 int o2_xtent = o2_e - o2_s;
152 if (o1_xtent == o2_xtent)
154 if (o1_cat == scoreCategory(EXP_CATEGORIES.get(0)))
156 if (o1_prov.equals(o2_prov)) {
157 if ("PDBE".equals(o1_prov)) {
158 if (eitherNull(idx_resol,o1data,o2data))
160 return nonNullFirst(idx_resol,o1data,o2data);
162 // experimental structures, so rank on quality
163 double o1_res = (Double) o1data[idx_resol];
164 double o2_res = (Double) o2data[idx_resol];
165 return (o2_res < o1_res) ? 1 : (o2_res == o1_res) ? 0 : -1;
167 return 0; // no change in order
170 // PDBe always ranked above all other experimentally determined categories
171 return "PDBE".equals(o1_prov) ? -1 : "PDBE".equals(o2_prov) ? 1 : 0;
176 if (eitherNull(idx_mqual,o1data, o2data)) {
177 return nonNullFirst(idx_mqual, o1data, o2data);
179 // models, so rank on qmean - b
180 double o1_mq = (Double) o1data[idx_mqual];
181 double o2_mq = (Double) o2data[idx_mqual];
182 return (o2_mq < o1_mq) ? 1 : (o2_mq == o1_mq) ? 0 : -1;
187 return o1_xtent - o2_xtent;
197 return o2_cat - o1_cat;
201 private int nonNullFirst(int idx_resol, Object[] o1data,
204 return o1data[idx_resol] == o2data[idx_resol] ? 0: o1data[idx_resol] != null ? -1 : 1;
207 private boolean eitherNull(int idx_resol, Object[] o1data,
210 return (o1data[idx_resol] == null || o2data[idx_resol]==null);
214 public boolean equals(Object obj)
216 return super.equals(obj);
219 return filteredResponse;
223 * return list of structures to be marked as selected for this sequence
224 * according to given criteria
226 * @param filteredStructures
227 * - sorted, filtered structures from getFilteredResponse
230 public List<FTSData> selectStructures(List<FTSData> filteredStructures)
232 List<FTSData> selected = new ArrayList<FTSData>();
233 BitSet cover = new BitSet();
234 cover.set(seq.getStart(), seq.getEnd());
235 // walk down the list of structures, selecting some to add to selected
236 for (FTSData structure : filteredStructures)
238 Object[] odata = structure.getSummaryData();
239 int o1_s = (Integer) odata[idx_ups];
240 int o1_e = (Integer) odata[idx_upe];
241 int o1_cat = scoreCategory((String) odata[idx_mcat]);
242 BitSet scover = new BitSet();
243 // measure intersection
244 scover.set(o1_s, o1_e);
246 if (scover.cardinality() > 4)
248 selected.add(structure);
249 // clear the range covered by this structure
250 cover.andNot(scover);
253 if (selected.size()==0)
257 // final step is to sort on length - this might help the superposition
259 Collections.sort(selected, new Comparator<FTSData>()
262 public int compare(FTSData o1, FTSData o2)
264 Object[] o1data = o1.getSummaryData();
265 Object[] o2data = o2.getSummaryData();
266 int o1_xt = ((Integer) o1data[idx_upe])
267 - ((Integer) o1data[idx_ups]);
268 int o1_cat = scoreCategory((String) o1data[idx_mcat]);
269 int o2_xt = ((Integer) o2data[idx_upe] - (Integer) o2data[idx_ups]);
270 int o2_cat = scoreCategory((String) o2data[idx_mcat]);
271 return o2_xt - o1_xt;
275 ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE))
277 return selected.subList(0, 1);