From 4fc80882cbf9f5624e7235459de51aab4df2c642 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 3 Sep 2021 15:37:29 +0100
Subject: [PATCH] JAL-3829 JAL-3865 StructureChooserQuerySource implementation
 now dependent on the type of sequences and whether they
 have uniprot sequence IDs

---
 src/jalview/gui/StructureChooser.java              |    2 +-
 .../StructureChooserQuerySource.java               |   32 ++++++++++++++++++++
 2 files changed, 33 insertions(+), 1 deletion(-)

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 7a9da92..86158da 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -104,7 +104,7 @@ public class StructureChooser extends GStructureChooser
   {
     // which FTS engine to use
     data = StructureChooserQuerySource
-            .getTDBfts();
+            .getQuerySourceFor(selectedSeqs);
     initDialog();
     
     this.ap = ap;
diff --git a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
index 733e6fc..4faa2de 100644
--- a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
@@ -206,4 +206,36 @@ public abstract class StructureChooserQuerySource
    *         will be constructed with 'addSeparator==true'
    */
   public abstract List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER);
+
+  /**
+   * construct a structure chooser query source for the given set of sequences
+   * @param selectedSeqs
+   * @return PDBe or 3DB query source
+   */
+  public static StructureChooserQuerySource getQuerySourceFor(
+          SequenceI[] selectedSeqs)
+  {
+    ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource();
+    boolean hasUniprot=false;
+    boolean hasNA=false,hasProtein=false;
+    for (SequenceI seq:selectedSeqs)
+    {
+      hasNA|=!seq.isProtein();
+      hasProtein |= seq.isProtein();
+      if (seq.isProtein())
+      {
+        String query = tdbSource.buildQuery(seq);
+        if (query!=null && query.length()>0)
+        {
+          hasUniprot=true;
+        }
+      }
+    }
+    if (hasProtein && hasUniprot && !hasNA)
+    {
+      return tdbSource;
+    }
+    return new PDBStructureChooserQuerySource();
+  }
+
 }
\ No newline at end of file
-- 
1.7.10.2