JAL-1919 code improvement to make PDB sequence fetcher file format configurable....

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 2e396aa..89ba84b 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;
@@ -740,7 +741,12 @@ 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();
@@ -821,6 +827,21 @@ 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)