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",
29 private SequenceI seq;
31 private Collection<FTSData> collectedResults;
33 private FTSRestRequest lastTdbRequest;
41 private int idx_mqual;
43 private int idx_resol;
45 public TDBResultAnalyser(SequenceI seq,
46 Collection<FTSData> collectedResults,
47 FTSRestRequest lastTdbRequest)
50 this.collectedResults = collectedResults;
51 this.lastTdbRequest = lastTdbRequest;
52 idx_ups = lastTdbRequest.getFieldIndex("Uniprot Start");
53 idx_upe = lastTdbRequest.getFieldIndex("Uniprot End");
54 idx_mcat = lastTdbRequest.getFieldIndex("Model Category");
55 idx_mqual = lastTdbRequest.getFieldIndex("Confidence");
56 idx_resol = lastTdbRequest.getFieldIndex("Resolution");
58 private final int scoreCategory(String cat)
61 int idx = EXP_CATEGORIES.indexOf(cat.toUpperCase());
64 System.out.println("Unknown category: '" + cat + "'");
66 return -EXP_CATEGORIES.size() - idx;
70 * sorts records discovered by 3D beacons and excludes any that don't
71 * intersect with the sequence's start/end rage
75 public List<FTSData> getFilteredResponse()
77 List<FTSData> filteredResponse = new ArrayList<FTSData>();
79 // ignore anything outside the sequence region
80 for (FTSData row : collectedResults)
82 int up_s = (Integer) row.getSummaryData()[idx_ups];
83 int up_e = (Integer) row.getSummaryData()[idx_upe];
85 if (seq == row.getSummaryData()[0] && up_e > seq.getStart()
86 && up_s < seq.getEnd())
88 filteredResponse.add(row);
91 // sort according to decreasing length,
93 Collections.sort(filteredResponse, new Comparator<FTSData>()
98 public int compare(FTSData o1, FTSData o2)
100 Object[] o1data = o1.getSummaryData();
101 Object[] o2data = o2.getSummaryData();
102 int o1_s = (Integer) o1data[idx_ups];
103 int o1_e = (Integer) o1data[idx_upe];
104 int o1_cat = scoreCategory((String) o1data[idx_mcat]);
105 int o2_s = (Integer) o2data[idx_ups];
106 int o2_e = (Integer) o2data[idx_upe];
107 int o2_cat = scoreCategory((String) o2data[idx_mcat]);
109 if (o1_cat == o2_cat)
113 int o1_xtent = o1_e - o1_s;
114 int o2_xtent = o2_e - o2_s;
115 if (o1_xtent == o2_xtent)
117 if (o1_cat == scoreCategory(EXP_CATEGORIES.get(0)))
119 // experimental structures, so rank on quality
120 double o1_res = (Double) o1data[idx_resol];
121 double o2_res = (Double) o2data[idx_resol];
122 return (o2_res < o1_res) ? 1 : (o2_res == o1_res) ? 0 : -1;
126 // models, so rank on qmean
127 float o1_mq = (Float) o1data[idx_mqual];
128 float o2_mq = (Float) o2data[idx_mqual];
129 return (o2_mq < o1_mq) ? 1 : (o2_mq == o1_mq) ? 0 : -1;
134 return o1_xtent - o2_xtent;
144 return o2_cat - o1_cat;
149 public boolean equals(Object obj)
151 return super.equals(obj);
154 return filteredResponse;
158 * return list of structures to be marked as selected for this sequence according to given criteria
159 * @param filteredStructures - sorted, filtered structures from getFilteredResponse
162 public List<FTSData> selectStructures(List<FTSData> filteredStructures)
164 List<FTSData> selected = new ArrayList<FTSData>();
165 BitSet cover = new BitSet();
166 cover.set(seq.getStart(),seq.getEnd());
167 // walk down the list of structures, selecting some to add to selected
168 for (FTSData structure:filteredStructures)
170 Object[] odata=structure.getSummaryData();
171 int o1_s = (Integer) odata[idx_ups];
172 int o1_e = (Integer) odata[idx_upe];
173 int o1_cat = scoreCategory((String) odata[idx_mcat]);
174 BitSet scover = new BitSet();
175 // measure intersection
176 scover.set(o1_s,o1_e);
178 if (scover.cardinality()>4)
180 selected.add(structure);
181 // clear the range covered by this structure
182 cover.andNot(scover);
185 // final step is to sort on length - this might help the superposition process
186 Collections.sort(selected,new Comparator<FTSData>()
189 public int compare(FTSData o1, FTSData o2)
191 Object[] o1data = o1.getSummaryData();
192 Object[] o2data = o2.getSummaryData();
193 int o1_xt = ((Integer) o1data[idx_upe]) - ((Integer) o1data[idx_ups]);
194 int o1_cat = scoreCategory((String) o1data[idx_mcat]);
195 int o2_xt = ((Integer) o2data[idx_upe]-(Integer) o2data[idx_ups]);
196 int o2_cat = scoreCategory((String) o2data[idx_mcat]);