JAL-4311 populate PDBEntry with 3d-beacons confidence score type/version - just need...

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index ae8523d..4acb65b 100755 (executable)
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -560,6 +560,10 @@ public class PDBEntry
 
   private static final String MODELPAGE = "PROVIDERPAGE";
 
+  private static final String TEMPFAC_TYPE = "TFTYPE";
+
+  private static final String TEMPFAC_TYPE_VERSION = "TFTYPE_V";
+
   /**
    * Permanent URI for retrieving the original structure data
    * 
@@ -644,4 +648,29 @@ public class PDBEntry
   {
     return sf != null && sf.inFile != null && sf.inFile.exists();
   }
+
+  public void setTempFacType(String strucTfType)
+  {
+    setProperty(TEMPFAC_TYPE,strucTfType);
+  }
+  public void setTempFacTypeVersion(String strucTfTypeVersion)
+  {
+    setProperty(TEMPFAC_TYPE_VERSION,strucTfTypeVersion);
+  }
+  public String getTempFacType()
+  {
+    return (String) getProperty(TEMPFAC_TYPE);
+  }
+  public String getTempFacTypeVersion()
+  {
+    return (String) getProperty(TEMPFAC_TYPE_VERSION);
+  }
+  public boolean hasTempFacType()
+  {
+    return _hasProperty(TEMPFAC_TYPE);
+  }
+  public boolean hasTempFacTypeVersion()
+  {
+    return _hasProperty(TEMPFAC_TYPE_VERSION);
+  }
 }

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 8135019..9942fcf 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1249,22 +1249,17 @@ public class StructureChooser extends GStructureChooser
       @Override
       public void run()
       {
-        FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
-                .getSelectedItem());
+        FilterOption selectedFilterOpt = getSelectedFilterOption();
         String currentView = selectedFilterOpt.getView();
         JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
                 : tbl_local_pdb;
 
         if (currentView == VIEWS_FILTER)
         {
-          int[] selectedRows = restable.getSelectedRows();
-          PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
-          List<SequenceI> selectedSeqsToView = new ArrayList<>();
-          pdbEntriesToView = data.collectSelectedRows(restable,
-                  selectedRows, selectedSeqsToView);
 
-          SequenceI[] selectedSeqs = selectedSeqsToView
-                  .toArray(new SequenceI[selectedSeqsToView.size()]);
+          Object[] seqsAndPdb = collectSelectedSeqsAndPDBEntries();
+          SequenceI[] selectedSeqs=(SequenceI[]) seqsAndPdb[0];
+          PDBEntry[] pdbEntriesToView = (PDBEntry[])seqsAndPdb[1];
           sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
                   selectedSeqs);
         }
@@ -1375,6 +1370,34 @@ public class StructureChooser extends GStructureChooser
   }
 
   /**
+   * collect selected structures from FTS search (PDB and TDB queries)
+   * @return Object[] { SequenceI[], PDBEntry[] } or null 
+   */
+  protected Object[] collectSelectedSeqsAndPDBEntries()
+  {
+    if (getSelectedFilterOption()==null || getSelectedFilterOption().getView() != VIEWS_FILTER)
+    {
+      return null;
+    }
+    JTable restable = getResultTable();
+    int[] selectedRows = restable.getSelectedRows();
+    PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+    List<SequenceI> selectedSeqsToView = new ArrayList<>();
+    pdbEntriesToView = data.collectSelectedRows(restable,
+            selectedRows, selectedSeqsToView);
+
+    SequenceI[] selectedSeqs = selectedSeqsToView
+            .toArray(new SequenceI[selectedSeqsToView.size()]);
+    return new Object[] { selectedSeqs,pdbEntriesToView};
+  }
+
+  private FilterOption getSelectedFilterOption()
+  {
+    return ((FilterOption) cmb_filterOption
+            .getSelectedItem());
+  }
+
+  /**
    * Answers a structure viewer (new or existing) configured to superimpose
    * added structures or not according to the user's choice
    * 

diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index 76ef85f..349d467 100644 (file)
--- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@ -387,6 +387,9 @@ public class ThreeDBStructureChooserQuerySource
     int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
     int humanUrl = restable.getColumn("Page URL").getModelIndex();
     int modelformat = restable.getColumn("Model Format").getModelIndex();
+    int tftype = restable.getColumn("Confidence Score Type").getModelIndex();
+    int tftypev = restable.getColumn("Confidence Score Version").getModelIndex();
+    
     final int up_start_idx = restable.getColumn("Uniprot Start")
             .getModelIndex();
     final int up_end_idx = restable.getColumn("Uniprot End")
@@ -424,7 +427,8 @@ public class ThreeDBStructureChooserQuerySource
       String modelPage = humanUrl < 1 ? null
               : (String) restable.getValueAt(row, humanUrl);
       String strucFormat = restable.getValueAt(row, modelformat).toString();
-
+      String strucTfType = tftype<1 ? null : restable.getValueAt(row, tftype)==null ? null : restable.getValueAt(row, tftype).toString();
+      String strucTfType_v = tftypev<1 ? null : restable.getValueAt(row, tftypev)==null ? null : restable.getValueAt(row, tftypev).toString();
       SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
               refSeqColIndex);
       selectedSeqsToView.add(selectedSeq);
@@ -457,6 +461,20 @@ public class ThreeDBStructureChooserQuerySource
         {
           pdbEntry.setProviderPage(modelPage);
         }
+        try
+        {
+          if (strucTfType!=null && "".equals(strucTfType)) {
+            pdbEntry.setTempFacType(strucTfType);
+          }
+          if (strucTfType_v!=null && "".equals(strucTfType_v)) {
+          pdbEntry.setTempFacTypeVersion(strucTfType_v);
+          }
+        } catch (Exception q)
+        {
+          Console.warn("Unknown filetype for 3D Beacons Model from: "
+                  + strucFormat + " - " + pdbIdStr + " - " + modelPage);
+        }
+
         selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
       }
       pdbEntriesToView[count++] = pdbEntry;

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index dd5cd4c..66760a2 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -235,6 +235,20 @@ public class StructureChooserTest
             "discoveredStructuresSet");
     assertNotNull(ss);
     assertTrue(ss.size() > 0);
+    
+    sc.promptForTDBFetch(true);
+    
+    // check collation
+    Object[] sqandpdb = sc.collectSelectedSeqsAndPDBEntries();
+    assertNotNull(sqandpdb);
+    SequenceI[] selsq = (SequenceI[]) sqandpdb[0];
+    PDBEntry[] selpdb = (PDBEntry[]) sqandpdb[1];
+    assertNotNull(selsq);
+    assertNotNull(selpdb);
+    assertEquals(1, selsq.length);
+    assertEquals(1, selpdb.length);
+    
+    
   }
 
   private void ThreadwaitFor(int i, StructureChooser sc)