From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 6 Jul 2023 17:17:14 +0000 (+0100)
Subject: JAL-629 liberal defensive coding, comments about refactoring and DEBUG output for... 
X-Git-Tag: Release_2_11_3_0~12^2~6
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fb1fb73bd1e6b08de09932c98d39b847dda1cf9a;hp=b101d3b57771a1c8bf2314e1a29748e23b23d3c0;p=jalview.git

JAL-629 liberal defensive coding, comments about refactoring and DEBUG output for --structureimage
---

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index e77e45d..84effe0 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -574,17 +574,22 @@ public class Commands
             Console.error("Failed to import and open structure view.");
             continue;
           }
-          try {
+          try
           {
-            while (sv.isBusy())
-              Thread.sleep(25);
+            {
+              while (sv.isBusy())
+                Thread.sleep(25);
+              if (sv.isBusy())
+              {
+                Console.debug(
+                        "Waiting for viewer for " + structureFilepath);
+              }
             }
-          }
-          catch (Exception x)
+          } catch (Exception x)
           {
-            
-          }
 
+          }
+          Console.debug("Successfully opened viewer for "+structureFilepath);
           String structureImageFilename = ArgParser.getValueFromSubValOrArg(
                   avm, av, Arg.STRUCTUREIMAGE, subVals);
           if (sv != null && structureImageFilename != null)
@@ -624,12 +629,13 @@ public class Commands
             }
             BitmapImageSizing userBis = ImageMaker
                     .parseScaleWidthHeightStrings(scale, width, height);
+            // TODO MAKE THIS VIEWER INDEPENDENT!!
             switch (StructureViewer.getViewerType())
             {
             case JMOL:
               try
               {
-                Thread.sleep(1000);
+                Thread.sleep(1000); // WHY ???
               } catch (InterruptedException e)
               {
                 // TODO Auto-generated catch block
@@ -641,8 +647,11 @@ public class Commands
               {
                 AppJmol jmol = (AppJmol) sview;
                 try { 
+                  Console.debug("Rendering image to "+structureImageFile);
                   jmol.makePDBImage(structureImageFile, imageType, renderer,
                         userBis);
+                  Console.debug("Finished Rendering image to "+structureImageFile);
+
                 }
                 catch (ImageOutputException ioexc)
                 {