JAL-3829 some providers don’t provide model quality, some experimental methods don...

diff --git a/src/jalview/gui/structurechooser/TDBResultAnalyser.java b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
index 06dbe2d..ffac9c4 100644 (file)
--- a/src/jalview/gui/structurechooser/TDBResultAnalyser.java
+++ b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
@@ -23,8 +23,8 @@ public class TDBResultAnalyser
    */
   private static List<String> EXP_CATEGORIES = Arrays
           .asList(new String[]
-          { "EXPERIMENTALLY DETERMINED", "DEEP-LEARNING",
-              "TEMPLATE-BASED" });
+          { "EXPERIMENTALLY DETERMINED", "DEEP-LEARNING", "TEMPLATE-BASED",
+              "AB-INITIO", "CONFORMATIONAL ENSEMBLE" });
 
   private SequenceI seq;
 
@@ -45,17 +45,19 @@ public class TDBResultAnalyser
   /**
    * selection model
    */
-  private String filter=null;
+  private String filter = null;
+
   /**
    * limit to particular source
    */
-  private String sourceFilter=null;
+  private String sourceFilter = null;
 
   private int idx_mprov;
 
   public TDBResultAnalyser(SequenceI seq,
           Collection<FTSData> collectedResults,
-          FTSRestRequest lastTdbRequest, String fieldToFilterBy, String string)
+          FTSRestRequest lastTdbRequest, String fieldToFilterBy,
+          String string)
   {
     this.seq = seq;
     this.collectedResults = collectedResults;
@@ -69,13 +71,27 @@ public class TDBResultAnalyser
     idx_mqual = lastTdbRequest.getFieldIndex("Confidence");
     idx_resol = lastTdbRequest.getFieldIndex("Resolution");
   }
-  private final int scoreCategory(String cat)
+
+  /**
+   * 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)
   {
-    // TODO: make quicker
-    int idx = EXP_CATEGORIES.indexOf(cat.toUpperCase());
+    if (cat == null)
+    {
+      return 0;
+    }
+    String upper_cat = cat.toUpperCase();
+    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;
   }
@@ -96,6 +112,9 @@ public class TDBResultAnalyser
       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()
@@ -117,9 +136,12 @@ public class TDBResultAnalyser
         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();
         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();
+        
 
         if (o1_cat == o2_cat)
         {
@@ -131,14 +153,30 @@ public class TDBResultAnalyser
             {
               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
               {
-                // models, so rank on qmean
+                if (eitherNull(idx_mqual,o1data, o2data)) {
+                  return nonNullFirst(idx_mqual, o1data, o2data);
+                }
+                // models, so rank on qmean - b
                 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;
@@ -160,6 +198,18 @@ public class TDBResultAnalyser
         }
       }
 
+      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)
       {
@@ -170,49 +220,55 @@ public class TDBResultAnalyser
   }
 
   /**
-   * return list of structures to be marked as selected for this sequence according to given criteria
-   * @param filteredStructures - sorted, filtered structures from getFilteredResponse
+   * 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());
+    cover.set(seq.getStart(), seq.getEnd());
     // walk down the list of structures, selecting some to add to selected
-    for (FTSData structure:filteredStructures)
+    for (FTSData structure : filteredStructures)
     {
-      Object[] odata=structure.getSummaryData();
+      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.set(o1_s, o1_e);
       scover.and(cover);
-      if (scover.cardinality()>4)
+      if (scover.cardinality() > 4)
       {
         selected.add(structure);
         // clear the range covered by this structure
-        cover.andNot(scover); 
+        cover.andNot(scover);
       }
     }
-    // final step is to sort on length - this might help the superposition process
-    Collections.sort(selected,new Comparator<FTSData>()
+    // 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_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_xt = ((Integer) o2data[idx_upe] - (Integer) o2data[idx_ups]);
         int o2_cat = scoreCategory((String) o2data[idx_mcat]);
-        return o2_xt-o1_xt;
+        return o2_xt - o1_xt;
       }
     });
-    if (filter.equals(ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE))
+    if (filter.equals(
+            ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE))
     {
       return selected.subList(0, 1);
     }