From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 20 Oct 2023 15:57:29 +0000 (+0100)
Subject: JAL-4298 Remove a stray return in the processGroovyScript method. Mildy improve a... 
X-Git-Tag: Release_2_11_4_0~131^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bd2ad93a3ea4075bc45528e3505e9510ffde835d;p=jalview.git

JAL-4298 Remove a stray return in the processGroovyScript method. Mildy improve a groovy example. Ensure consistent setting of groovy variables with JalviewObjectI fields. Update the currentAlFrame when run from Calculate menu.
---

diff --git a/examples/groovy/stripUniprotPrefixes.groovy b/examples/groovy/stripUniprotPrefixes.groovy
index 2792604..5a01da4 100644
--- a/examples/groovy/stripUniprotPrefixes.groovy
+++ b/examples/groovy/stripUniprotPrefixes.groovy
@@ -47,5 +47,6 @@ for (ala in af)
 			}
 		}
 	}
+	ala.repaint();
 }
 	
diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 3006f1f..e02d132 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -851,7 +851,6 @@ public class Commands
     if (af == null)
     {
       addWarn("Groovy script does not have an alignment window.  Proceeding with caution!");
-      return;
     }
 
     if (avm.containsArg(Arg.GROOVY))
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 783f533..83efe7d 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1753,8 +1753,8 @@ public class Jalview implements JalviewObjectI
     {
       JalviewObjectI j = new JalviewObject(this);
       Map<String, java.lang.Object> vbinding = new HashMap<>();
-      vbinding.put("Jalview", j);
-      vbinding.put("currentAlFrame",
+      vbinding.put(JalviewObjectI.jalviewObjectName, j);
+      vbinding.put(JalviewObjectI.currentAlFrameName,
               af != null ? af : getCurrentAlignFrame());
       Binding gbinding = new Binding(vbinding);
       GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
diff --git a/src/jalview/bin/groovy/JalviewObjectI.java b/src/jalview/bin/groovy/JalviewObjectI.java
index 775ab2a..f365d30 100644
--- a/src/jalview/bin/groovy/JalviewObjectI.java
+++ b/src/jalview/bin/groovy/JalviewObjectI.java
@@ -8,7 +8,9 @@ public interface JalviewObjectI
 
   public AlignFrame getCurrentAlignFrame();
 
-  public static AlignFrame currentAlFrame = null;
+  public final static String currentAlFrameName = "currentAlFrame";
+
+  public final static String jalviewObjectName = "Jalview";
 
   public void quit();
 }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ae14539..ac8ffb9 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -95,6 +95,7 @@ import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
+import jalview.bin.groovy.JalviewObjectI;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -5969,6 +5970,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       try
       {
+        console.setVariable(JalviewObjectI.currentAlFrameName, this);
         console.runScript();
       } catch (Exception ex)
       {
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index b1f9000..1cedf3b 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -2663,8 +2663,9 @@ public class Desktop extends jalview.jbgui.GDesktop
     {
       JalviewObjectI j = new JalviewObject(this);
       groovyConsole = new groovy.console.ui.Console();
-      groovyConsole.setVariable("Jalview", j);
-      groovyConsole.setVariable("currentAlFrame", getCurrentAlignFrame());
+      groovyConsole.setVariable(JalviewObjectI.jalviewObjectName, j);
+      groovyConsole.setVariable(JalviewObjectI.currentAlFrameName,
+              getCurrentAlignFrame());
       groovyConsole.run();
 
       /*