Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_...

[jalview.git] / src / jalview / io / BioJsHTMLOutput.java

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 48988cf..13bfb8c 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -20,13 +20,6 @@
  */
 package jalview.io;
 
-import jalview.bin.Cache;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.OOMWarning;
-import jalview.json.binding.biojs.BioJSReleasePojo;
-import jalview.json.binding.biojs.BioJSRepositoryPojo;
-import jalview.util.MessageManager;
-
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.File;
@@ -39,6 +32,13 @@ import java.net.URL;
 import java.util.Objects;
 import java.util.TreeMap;
 
+import jalview.bin.Cache;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.OOMWarning;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
+import jalview.util.MessageManager;
+
 public class BioJsHTMLOutput extends HTMLOutput
 {
   private static File currentBJSTemplateFile;
@@ -51,9 +51,9 @@ public class BioJsHTMLOutput extends HTMLOutput
   public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
           .getDefault("biojs_template_directory", DEFAULT_DIR);
 
-  public static final String BJS_TEMPLATE_GIT_REPO = Cache
-          .getDefault("biojs_template_git_repo",
-                  "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
+  public static final String BJS_TEMPLATE_GIT_REPO = Cache.getDefault(
+          "biojs_template_git_repo",
+          "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
 
   public BioJsHTMLOutput(AlignmentPanel ap)
   {
@@ -138,8 +138,9 @@ public class BioJsHTMLOutput extends HTMLOutput
       {
         if (!biojsDirectory.mkdirs())
         {
-          System.out.println("Couldn't create local directory : "
-                  + BJS_TEMPLATES_LOCAL_DIRECTORY);
+          jalview.bin.Console
+                  .outPrintln("Couldn't create local directory : "
+                          + BJS_TEMPLATES_LOCAL_DIRECTORY);
           return;
         }
       }
@@ -264,8 +265,9 @@ public class BioJsHTMLOutput extends HTMLOutput
 
     } catch (OutOfMemoryError err)
     {
-      System.out.println("########################\n" + "OUT OF MEMORY "
-              + generatedFile + "\n" + "########################");
+      jalview.bin.Console
+              .outPrintln("########################\n" + "OUT OF MEMORY "
+                      + generatedFile + "\n" + "########################");
       new OOMWarning("Creating Image for " + generatedFile, err);
     } catch (Exception e)
     {
@@ -276,4 +278,10 @@ public class BioJsHTMLOutput extends HTMLOutput
 
   }
 
+  @Override
+  public void run(String s)
+  {
+    run();
+  }
+
 }