JAL-2045 JAL-2047 improvement for sorting PDB quality measure numerically, and improv...

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index d313002..f38f267 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -44,6 +44,7 @@ import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Objects;
+import java.util.Vector;
 
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
@@ -399,18 +400,6 @@ public class StructureChooser extends GStructureChooser implements
                 .getStructureSummaryFields();
         Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
         HashSet<String> errors = new HashSet<String>();
-        // try
-        // {
-        // PDBDocField fiterField = PDBRestClient
-        // .getPDBDocFieldByCode(fieldToFilterBy);
-        // if (!wantedFields.contains(fiterField))
-        // {
-        // wantedFields.add(fiterField);
-        // }
-        // } catch (Exception e)
-        // {
-        // e.printStackTrace();
-        // }
 
         for (SequenceI seq : selectedSequences)
         {
@@ -469,6 +458,10 @@ public class StructureChooser extends GStructureChooser implements
           tbl_summary.setModel(PDBRestResponse.getTableModel(
                   lastPdbRequest, reorderedStructuresSet));
 
+          PDBRestResponse.configureTableColumn(tbl_summary, wantedFields);
+          tbl_summary.getColumn("Ref Sequence").setPreferredWidth(120);
+          tbl_summary.getColumn("Ref Sequence").setMinWidth(100);
+          tbl_summary.getColumn("Ref Sequence").setMaxWidth(200);
           // Update table selection model here
           tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
           mainFrame.setTitle(MessageManager.formatMessage(
@@ -752,7 +745,12 @@ public class StructureChooser extends GStructureChooser implements
         SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
                 refSeqColIndex);
         selectedSeqsToView.add(selectedSeq);
-        PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
+            PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
+            if (pdbEntry == null)
+            {
+              pdbEntry = getFindEntry(pdbIdStr,
+                      selectedSeq.getAllPDBEntries());
+            }
         if (pdbEntry == null)
         {
           pdbEntry = new PDBEntry();
@@ -833,6 +831,21 @@ public class StructureChooser extends GStructureChooser implements
     }).start();
   }
 
+  private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+  {
+    Objects.requireNonNull(id);
+    Objects.requireNonNull(pdbEntries);
+    PDBEntry foundEntry = null;
+    for (PDBEntry entry : pdbEntries)
+    {
+      if (entry.getId().equalsIgnoreCase(id))
+      {
+        return entry;
+      }
+    }
+    return foundEntry;
+  }
+
   private void launchStructureViewer(StructureSelectionManager ssm,
           final PDBEntry[] pdbEntriesToView,
           final AlignmentPanel alignPanel, SequenceI[] sequences)