X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2Fstructurechooser%2FTDBResultAnalyser.java;fp=src%2Fjalview%2Fgui%2Fstructurechooser%2FTDBResultAnalyser.java;h=06dbe2daddb7ddb3cfd73f2196fe1a3fe26ac2cf;hb=18344fcaeb3ee1c80b1c1de907ebe24f1ead18e4;hp=0000000000000000000000000000000000000000;hpb=bc7283e7d80b1f7f5fb7d95c51b96bb3af31593d;p=jalview.git

diff --git a/src/jalview/gui/structurechooser/TDBResultAnalyser.java b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
new file mode 100644
index 0000000..06dbe2d
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+++ b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
@@ -0,0 +1,222 @@
+package jalview.gui.structurechooser;
+
+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" });
+
+  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");
+  }
+  private final int scoreCategory(String cat)
+  {
+    // TODO: make quicker
+    int idx = EXP_CATEGORIES.indexOf(cat.toUpperCase());
+    if (idx == -1)
+    {
+      System.out.println("Unknown category: '" + cat + "'");
+    }
+    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];
+      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]);
+        int o2_s = (Integer) o2data[idx_ups];
+        int o2_e = (Integer) o2data[idx_upe];
+        int o2_cat = scoreCategory((String) o2data[idx_mcat]);
+
+        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)))
+              {
+                // 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
+              {
+                // models, so rank on qmean
+                float o1_mq = (Float) o1data[idx_mqual];
+                float o2_mq = (Float) 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;
+        }
+      }
+
+      @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
+    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); 
+      }
+    }
+    // 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;
+  }
+
+}