JAL-4290 Move some annotation visibility settings to after opening a structure. Set...

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index e01d40a..dbc5e23 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -210,8 +210,13 @@ public class Commands
 
     Boolean isError = Boolean.valueOf(false);
 
-    // set wrap scope here so it can be applied after structures are opened
+    // set wrap, showSSAnnotations, showAnnotations and hideTFrows scope here so
+    // it can be applied after structures are opened
     boolean wrap = false;
+    boolean showSSAnnotations = false;
+    boolean showAnnotations = false;
+    boolean hideTFrows = false;
+    AlignFrame af = null;
 
     if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
     {
@@ -220,7 +225,6 @@ public class Commands
 
       boolean first = true;
       boolean progressBarSet = false;
-      AlignFrame af;
       // Combine the APPEND and OPEN files into one list, along with whether it
       // was APPEND or OPEN
       List<ArgValue> openAvList = new ArrayList<>();
@@ -392,53 +396,17 @@ public class Commands
           }
 
           // Show secondary structure annotations?
-          boolean showSSAnnotations = avm.getFromSubValArgOrPref(
+          showSSAnnotations = avm.getFromSubValArgOrPref(
                   Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
                   "STRUCT_FROM_PDB", true);
-
           // Show sequence annotations?
-          boolean showAnnotations = avm.getFromSubValArgOrPref(
-                  Arg.SHOWANNOTATIONS, av.getSubVals(), null,
-                  "SHOW_ANNOTATIONS", true);
-
-          boolean hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
-          final AlignFrame _af = af;
-          // many of jalview's format/layout methods are only thread safe on the
-          // swingworker thread.
-          // all these methods should be on the alignViewController so it can
-          // coordinate such details
-          try
-          {
-            SwingUtilities.invokeAndWait(new Runnable()
-            {
+          showAnnotations = avm.getFromSubValArgOrPref(Arg.SHOWANNOTATIONS,
+                  av.getSubVals(), null, "SHOW_ANNOTATIONS", true);
+          // hide the Temperature Factor row?
+          hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
 
-              @Override
-              public void run()
-              {
-                _af.setAnnotationsVisibility(showSSAnnotations, true,
-                        false);
-
-                _af.setAnnotationsVisibility(showAnnotations, false, true);
-
-                // show temperature factor annotations?
-                if (hideTFrows)
-                {
-                  // do this better (annotation types?)
-                  List<String> hideThese = new ArrayList<>();
-                  hideThese.add("Temperature Factor");
-                  hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
-                  AlignmentUtils.showOrHideSequenceAnnotations(
-                          _af.getCurrentView().getAlignment(), hideThese,
-                          null, false, false);
-                }
-              }
-            });
-          } catch (Exception x)
-          {
-            Console.warn(
-                    "Unexpected exception adjusting annotation row visibility.",
-                    x);
-          }
+          // showSSAnnotations, showAnnotations, hideTFrows used after opening
+          // structure
 
           // wrap alignment? do this last for formatting reasons
           wrap = avm.getFromSubValArgOrPref(Arg.WRAP, sv, null,
@@ -496,8 +464,10 @@ public class Commands
     // open the structure (from same PDB file or given PDBfile)
     if (!avm.getBoolean(Arg.NOSTRUCTURE))
     {
-
-      AlignFrame af = afMap.get(id);
+      if (af == null)
+      {
+        af = afMap.get(id);
+      }
       if (avm.containsArg(Arg.STRUCTURE))
       {
         commandArgsProvided = true;
@@ -867,10 +837,47 @@ public class Commands
       }
     }
 
-    if (wrap)
+    if (af == null)
     {
+      af = afMap.get(id);
+    }
+    // many of jalview's format/layout methods are only thread safe on the
+    // swingworker thread.
+    // all these methods should be on the alignViewController so it can
+    // coordinate such details
+    if (headless)
+    {
+      showOrHideAnnotations(af, showSSAnnotations, showAnnotations,
+              hideTFrows);
+    }
+    else
+    {
+      try
+      {
+        AlignFrame _af = af;
+        final boolean _showSSAnnotations = showSSAnnotations;
+        final boolean _showAnnotations = showAnnotations;
+        final boolean _hideTFrows = hideTFrows;
+        SwingUtilities.invokeAndWait(() -> {
+          showOrHideAnnotations(_af, _showSSAnnotations, _showAnnotations,
+                  _hideTFrows);
+        }
 
-      AlignFrame af = afMap.get(id);
+        );
+      } catch (Exception x)
+      {
+        Console.warn(
+                "Unexpected exception adjusting annotation row visibility.",
+                x);
+      }
+    }
+
+    if (wrap)
+    {
+      if (af == null)
+      {
+        af = afMap.get(id);
+      }
       if (af != null)
       {
         af.setWrapFormat(wrap, true);
@@ -897,6 +904,31 @@ public class Commands
     return theseArgsWereParsed && !isError;
   }
 
+  private static void showOrHideAnnotations(AlignFrame af,
+          boolean showSSAnnotations, boolean showAnnotations,
+          boolean hideTFrows)
+  {
+    Console.debug(
+            "##### Setting showSSAnnotations to " + showSSAnnotations);
+    Console.debug("##### Setting showAnnotations to " + showAnnotations);
+    Console.debug("##### Setting hideTFrows to " + hideTFrows);
+    af.setAnnotationsVisibility(showSSAnnotations, true, false);
+
+    af.setAnnotationsVisibility(showAnnotations, false, true);
+
+    // show temperature factor annotations?
+    if (hideTFrows)
+    {
+      // do this better (annotation types?)
+      List<String> hideThese = new ArrayList<>();
+      hideThese.add("Temperature Factor");
+      hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
+      AlignmentUtils.showOrHideSequenceAnnotations(
+              af.getCurrentView().getAlignment(), hideThese, null, false,
+              false);
+    }
+  }
+
   protected void processGroovyScript(String id)
   {
     ArgValuesMap avm = argParser.getLinkedArgs(id);