JAL-629 dispose of non-displaying StructureChooser, removes zombie entry in Window...

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index fc73c27..8423ed9 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;
@@ -67,6 +66,7 @@ import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
 import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.fts.service.threedbeacons.TDB_FTSData;
+import jalview.gui.StructureViewer.ViewerType;
 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
 import jalview.gui.structurechooser.StructureChooserQuerySource;
 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
@@ -346,7 +346,7 @@ public class StructureChooser extends GStructureChooser
     };
 
     // fetch db refs if OK pressed
-    final Callable discoverCanonicalDBrefs = () -> {
+    final Runnable discoverCanonicalDBrefs = () -> {
       btn_queryTDB.setEnabled(false);
       populateSeqsWithoutSourceDBRef();
 
@@ -368,14 +368,12 @@ 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);
@@ -1284,7 +1282,8 @@ public class StructureChooser extends GStructureChooser
           String pdbFilename = selectedPdbFileName;
 
           StructureChooser.openStructureFileForSequence(ssm, sc, ap,
-                  selectedSequence, true, pdbFilename, tft, paeFilename);
+                  selectedSequence, true, pdbFilename, tft, paeFilename,
+                  true);
         }
         SwingUtilities.invokeLater(new Runnable()
         {
@@ -1343,6 +1342,15 @@ public class StructureChooser extends GStructureChooser
           StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
           final AlignmentPanel alignPanel, SequenceI[] sequences)
   {
+    return launchStructureViewer(ssm, pdbEntriesToView, alignPanel,
+            sequences, null);
+  }
+
+  private StructureViewer launchStructureViewer(
+          StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
+          final AlignmentPanel alignPanel, SequenceI[] sequences,
+          ViewerType viewerType)
+  {
     long progressId = sequences.hashCode();
     setProgressBar(MessageManager
             .getString("status.launching_3d_structure_viewer"), progressId);
@@ -1407,7 +1415,8 @@ public class StructureChooser extends GStructureChooser
               MessageManager.getString(
                       "status.fetching_3d_structures_for_selected_entries"),
               progressId);
-      theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
+      theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel,
+              viewerType);
     }
     else
     {
@@ -1415,7 +1424,8 @@ public class StructureChooser extends GStructureChooser
               "status.fetching_3d_structures_for",
               pdbEntriesToView[0].getId()), progressId);
       // Can we pass a pre-computeMappinged pdbFile?
-      theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+      theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel,
+              viewerType);
     }
     setProgressBar(null, progressId);
     // remember the last viewer we used...
@@ -1656,20 +1666,21 @@ 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()
@@ -1716,43 +1727,52 @@ public class StructureChooser extends GStructureChooser
   public static void openStructureFileForSequence(
           StructureSelectionManager ssm, StructureChooser sc,
           AlignmentPanel ap, SequenceI seq, boolean prompt,
-          String sFilename, TFType tft, String paeFilename)
+          String sFilename, TFType tft, String paeFilename,
+          boolean doXferSettings)
   {
     openStructureFileForSequence(ssm, sc, ap, seq, prompt, sFilename, tft,
-            paeFilename, false, true);
+            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 showAnnotations)
+          boolean forceHeadless, boolean showRefAnnotations,
+          boolean doXferSettings, ViewerType viewerType)
   {
+    StructureViewer sv = null;
     boolean headless = forceHeadless;
     if (sc == null)
     {
-      headless = true;
+      // headless = true;
       prompt = false;
       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,
-            tft, paeFilename);
+            tft, paeFilename, doXferSettings);
 
     // if headless, "false" in the sc constructor above will avoid GUI behaviour
     // in sc.launchStructureViewer()
-    sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
-            new SequenceI[]
-            { seq });
+    if (!headless && !(viewerType == null))
+    {
+      sv = sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+              new SequenceI[]
+              { seq }, viewerType);
+    }
 
-    if (headless)
-      sc.mainFrame.dispose();
+    sc.mainFrame.dispose();
 
-    if (showAnnotations)
+    if (showRefAnnotations)
       showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+
+    return sv;
   }
 
   public static void showReferenceAnnotationsForSequence(AlignFrame af,