Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 6c68ee6..6fce984 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -33,7 +33,6 @@ import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
-import java.util.concurrent.Callable;
 import java.util.concurrent.Executors;
 
 import javax.swing.JCheckBox;
@@ -350,7 +349,7 @@ public class StructureChooser extends GStructureChooser
     };
 
     // fetch db refs if OK pressed
-    final Callable discoverCanonicalDBrefs = () -> {
+    final Runnable discoverCanonicalDBrefs = () -> {
       btn_queryTDB.setEnabled(false);
       populateSeqsWithoutSourceDBRef();
 
@@ -372,14 +371,12 @@ public class StructureChooser extends GStructureChooser
         // call finished action directly
         afterDbRefFetch.finished();
       }
-      return null;
     };
-    final Callable revertview = () -> {
+    final Runnable revertview = () -> {
       if (lastSelected != null)
       {
         cmb_filterOption.setSelectedItem(lastSelected);
       }
-      return null;
     };
     int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
             THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
@@ -1700,20 +1697,21 @@ public class StructureChooser extends GStructureChooser
   @Override
   public void setProgressBar(String message, long id)
   {
-    if (!Platform.isHeadless())
+    if (!Platform.isHeadless() && progressBar != null)
       progressBar.setProgressBar(message, id);
   }
 
   @Override
   public void registerHandler(long id, IProgressIndicatorHandler handler)
   {
-    progressBar.registerHandler(id, handler);
+    if (progressBar != null)
+      progressBar.registerHandler(id, handler);
   }
 
   @Override
   public boolean operationInProgress()
   {
-    return progressBar.operationInProgress();
+    return progressBar == null ? false : progressBar.operationInProgress();
   }
 
   public JalviewStructureDisplayI getOpenedStructureViewer()
@@ -1767,13 +1765,14 @@ public class StructureChooser extends GStructureChooser
             paeFilename, false, true, doXferSettings, null);
   }
 
-  public static void openStructureFileForSequence(
+  public static StructureViewer openStructureFileForSequence(
           StructureSelectionManager ssm, StructureChooser sc,
           AlignmentPanel ap, SequenceI seq, boolean prompt,
           String sFilename, TFType tft, String paeFilename,
           boolean forceHeadless, boolean showRefAnnotations,
           boolean doXferSettings, ViewerType viewerType)
   {
+    StructureViewer sv = null;
     boolean headless = forceHeadless;
     if (sc == null)
     {
@@ -1782,7 +1781,9 @@ public class StructureChooser extends GStructureChooser
       sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
     }
     if (ssm == null)
+    {
       ssm = ap.getStructureSelectionManager();
+    }
 
     PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
             sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
@@ -1791,15 +1792,18 @@ public class StructureChooser extends GStructureChooser
     // if headless, "false" in the sc constructor above will avoid GUI behaviour
     // in sc.launchStructureViewer()
     if (!headless && !(viewerType == null))
-      sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+    {
+      sv = sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
               new SequenceI[]
               { seq }, viewerType);
+    }
 
-    if (headless)
-      sc.mainFrame.dispose();
+    sc.mainFrame.dispose();
 
     if (showRefAnnotations)
       showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+
+    return sv;
   }
 
   public static void showReferenceAnnotationsForSequence(AlignFrame af,