--- /dev/null
+package jalview.gui.structurechooser;
+
+import java.util.Locale;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.core.FTSRestRequest;
+
+public class TDBResultAnalyser
+{
+
+ /**
+ * model categories - update as needed. warnings output if unknown types
+ * encountered.
+ *
+ * Order denotes 'trust'
+ */
+ private static List<String> EXP_CATEGORIES = Arrays
+ .asList(new String[]
+ { "EXPERIMENTALLY DETERMINED", "DEEP-LEARNING", "TEMPLATE-BASED",
+ "AB-INITIO", "CONFORMATIONAL ENSEMBLE" });
+
+ private SequenceI seq;
+
+ private Collection<FTSData> collectedResults;
+
+ private FTSRestRequest lastTdbRequest;
+
+ private int idx_ups;
+
+ private int idx_upe;
+
+ private int idx_mcat;
+
+ private int idx_mqual;
+
+ private int idx_resol;
+
+ /**
+ * selection model
+ */
+ private String filter = null;
+
+ /**
+ * limit to particular source
+ */
+ private String sourceFilter = null;
+
+ private int idx_mprov;
+
+ public TDBResultAnalyser(SequenceI seq,
+ Collection<FTSData> collectedResults,
+ FTSRestRequest lastTdbRequest, String fieldToFilterBy,
+ String string)
+ {
+ this.seq = seq;
+ this.collectedResults = collectedResults;
+ this.lastTdbRequest = lastTdbRequest;
+ this.filter = fieldToFilterBy;
+ this.sourceFilter = string;
+ idx_ups = lastTdbRequest.getFieldIndex("Uniprot Start");
+ idx_upe = lastTdbRequest.getFieldIndex("Uniprot End");
+ idx_mcat = lastTdbRequest.getFieldIndex("Model Category");
+ idx_mprov = lastTdbRequest.getFieldIndex("Provider");
+ idx_mqual = lastTdbRequest.getFieldIndex("Confidence");
+ idx_resol = lastTdbRequest.getFieldIndex("Resolution");
+ }
+
+ /**
+ * maintain and resolve categories to 'trust order' TODO: change the trust
+ * scheme to something comprehensible.
+ *
+ * @param cat
+ * @return 0 for null cat, less than zero for others
+ */
+ public final int scoreCategory(String cat)
+ {
+ if (cat == null)
+ {
+ return 0;
+ }
+ String upper_cat = cat.toUpperCase(Locale.ROOT);
+ int idx = EXP_CATEGORIES.indexOf(upper_cat);
+ if (idx == -1)
+ {
+ System.out.println("Unknown category: '" + cat + "'");
+ EXP_CATEGORIES.add(upper_cat);
+ idx = EXP_CATEGORIES.size() - 1;
+ }
+ return -EXP_CATEGORIES.size() - idx;
+ }
+
+ /**
+ * sorts records discovered by 3D beacons and excludes any that don't
+ * intersect with the sequence's start/end rage
+ *
+ * @return
+ */
+ public List<FTSData> getFilteredResponse()
+ {
+ List<FTSData> filteredResponse = new ArrayList<FTSData>();
+
+ // ignore anything outside the sequence region
+ for (FTSData row : collectedResults)
+ {
+ int up_s = (Integer) row.getSummaryData()[idx_ups];
+ int up_e = (Integer) row.getSummaryData()[idx_upe];
+ String provider = (String) row.getSummaryData()[idx_mprov];
+ String mcat = (String) row.getSummaryData()[idx_mcat];
+ // this makes sure all new categories are in the score array.
+ int scorecat = scoreCategory(mcat);
+ if (sourceFilter == null || sourceFilter.equals(provider))
+ {
+ if (seq == row.getSummaryData()[0] && up_e > seq.getStart()
+ && up_s < seq.getEnd())
+ {
+ filteredResponse.add(row);
+ }
+ }
+ }
+ // sort according to decreasing length,
+ // increasing start
+ Collections.sort(filteredResponse, new Comparator<FTSData>()
+ {
+ @Override
+ public int compare(FTSData o1, FTSData o2)
+ {
+ Object[] o1data = o1.getSummaryData();
+ Object[] o2data = o2.getSummaryData();
+ int o1_s = (Integer) o1data[idx_ups];
+ int o1_e = (Integer) o1data[idx_upe];
+ int o1_cat = scoreCategory((String) o1data[idx_mcat]);
+ String o1_prov= ((String) o1data[idx_mprov]).toUpperCase(Locale.ROOT);
+ int o2_s = (Integer) o2data[idx_ups];
+ int o2_e = (Integer) o2data[idx_upe];
+ int o2_cat = scoreCategory((String) o2data[idx_mcat]);
+ String o2_prov= ((String) o2data[idx_mprov]).toUpperCase(Locale.ROOT);
+
+
+ if (o1_cat == o2_cat)
+ {
+ if (o1_s == o2_s)
+ {
+ int o1_xtent = o1_e - o1_s;
+ int o2_xtent = o2_e - o2_s;
+ if (o1_xtent == o2_xtent)
+ {
+ if (o1_cat == scoreCategory(EXP_CATEGORIES.get(0)))
+ {
+ if (o1_prov.equals(o2_prov)) {
+ if ("PDBE".equals(o1_prov)) {
+ if (eitherNull(idx_resol,o1data,o2data))
+ {
+ return nonNullFirst(idx_resol,o1data,o2data);
+ }
+ // experimental structures, so rank on quality
+ double o1_res = (Double) o1data[idx_resol];
+ double o2_res = (Double) o2data[idx_resol];
+ return (o2_res < o1_res) ? 1 : (o2_res == o1_res) ? 0 : -1;
+ } else {
+ return 0; // no change in order
+ }
+ } else {
+ // PDBe always ranked above all other experimentally determined categories
+ return "PDBE".equals(o1_prov) ? -1 : "PDBE".equals(o2_prov) ? 1 : 0;
+ }
+ }
+ else
+ {
+ if (eitherNull(idx_mqual,o1data, o2data)) {
+ return nonNullFirst(idx_mqual, o1data, o2data);
+ }
+ // models, so rank on qmean - b
+ double o1_mq = (Double) o1data[idx_mqual];
+ double o2_mq = (Double) o2data[idx_mqual];
+ return (o2_mq < o1_mq) ? 1 : (o2_mq == o1_mq) ? 0 : -1;
+ }
+ }
+ else
+ {
+ return o1_xtent - o2_xtent;
+ }
+ }
+ else
+ {
+ return o1_s - o2_s;
+ }
+ }
+ else
+ {
+ return o2_cat - o1_cat;
+ }
+ }
+
+ private int nonNullFirst(int idx_resol, Object[] o1data,
+ Object[] o2data)
+ {
+ return o1data[idx_resol] == o2data[idx_resol] ? 0: o1data[idx_resol] != null ? -1 : 1;
+ }
+
+ private boolean eitherNull(int idx_resol, Object[] o1data,
+ Object[] o2data)
+ {
+ return (o1data[idx_resol] == null || o2data[idx_resol]==null);
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ return super.equals(obj);
+ }
+ });
+ return filteredResponse;
+ }
+
+ /**
+ * return list of structures to be marked as selected for this sequence
+ * according to given criteria
+ *
+ * @param filteredStructures
+ * - sorted, filtered structures from getFilteredResponse
+ *
+ */
+ public List<FTSData> selectStructures(List<FTSData> filteredStructures)
+ {
+ List<FTSData> selected = new ArrayList<FTSData>();
+ BitSet cover = new BitSet();
+ cover.set(seq.getStart(), seq.getEnd());
+ // walk down the list of structures, selecting some to add to selected
+ // TODO: could do simple DP - double loop to select largest number of
+ // structures covering largest number of sites
+ for (FTSData structure : filteredStructures)
+ {
+ Object[] odata = structure.getSummaryData();
+ int o1_s = (Integer) odata[idx_ups];
+ int o1_e = (Integer) odata[idx_upe];
+ int o1_cat = scoreCategory((String) odata[idx_mcat]);
+ BitSet scover = new BitSet();
+ // measure intersection
+ scover.set(o1_s, o1_e);
+ scover.and(cover);
+ if (scover.cardinality() > 4)
+ {
+ selected.add(structure);
+ // clear the range covered by this structure
+ cover.andNot(scover);
+ }
+ }
+ if (selected.size()==0)
+ {
+ return selected;
+ }
+ // final step is to sort on length - this might help the superposition
+ // process
+ Collections.sort(selected, new Comparator<FTSData>()
+ {
+ @Override
+ public int compare(FTSData o1, FTSData o2)
+ {
+ Object[] o1data = o1.getSummaryData();
+ Object[] o2data = o2.getSummaryData();
+ int o1_xt = ((Integer) o1data[idx_upe])
+ - ((Integer) o1data[idx_ups]);
+ int o1_cat = scoreCategory((String) o1data[idx_mcat]);
+ int o2_xt = ((Integer) o2data[idx_upe] - (Integer) o2data[idx_ups]);
+ int o2_cat = scoreCategory((String) o2data[idx_mcat]);
+ return o2_xt - o1_xt;
+ }
+ });
+ if (filter.equals(
+ ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE))
+ {
+ return selected.subList(0, 1);
+ }
+ return selected;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff