X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=c88d8ebe4252a9a8079f5f2137adb0e8178f1491;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=1be97f507c6004abdcb36cb395c880baff5c9e53;hpb=e60cacff9260c47c12cf34a7e191678cfc97d265;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 1be97f5..c88d8eb 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -20,7 +20,7 @@
  */
 package jalview.io;
 
-import jalview.exceptions.NoFileSelectedException;
+import jalview.bin.Cache;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.OOMWarning;
 import jalview.json.binding.biojs.BioJSReleasePojo;
@@ -41,7 +41,6 @@ import java.util.TreeMap;
 
 public class BioJsHTMLOutput extends HTMLOutput
 {
-
   private static File currentBJSTemplateFile;
 
   private static TreeMap<String, File> bioJsMSAVersions;
@@ -49,64 +48,18 @@ public class BioJsHTMLOutput extends HTMLOutput
   public static final String DEFAULT_DIR = System.getProperty("user.home")
           + File.separatorChar + ".biojs_templates" + File.separatorChar;
 
-  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
+  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
           .getDefault("biojs_template_directory", DEFAULT_DIR);
 
-  public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.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)
   {
-    super(ap);
+    super(ap, "BioJS MSA");
   }
 
-  @Override
-  public void exportHTML(String outputFile)
-  {
-    exportStarted();
-    try
-    {
-
-      if (outputFile == null)
-      {
-        outputFile = getOutputFile();
-      }
-      generatedFile = new File(outputFile);
-
-      String bioJSON = getBioJSONData();
-      String bioJSTemplateString = HTMLOutput.readFileAsString(getCurrentBJSTemplateFile());
-      String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
-              .replaceAll("#sequenceData#", bioJSON).toString();
-
-      PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
-              generatedFile));
-      out.print(generatedBioJsWithJalviewAlignmentAsJson);
-      out.flush();
-      out.close();
-      exportCompleted();
-      setProgressMessage(MessageManager.formatMessage(
-              "status.export_complete", "BioJS"));
-
-    } catch (NoFileSelectedException ex)
-    {
-      // do noting if no file was selected
-    } catch (OutOfMemoryError err)
-    {
-      System.out.println("########################\n" + "OUT OF MEMORY "
-              + outputFile + "\n" + "########################");
-      new OOMWarning("Creating Image for " + outputFile, err);
-    } catch (Exception e)
-    {
-      setProgressMessage(MessageManager.formatMessage(
-              "info.error_creating_file", "HTML"));
-      e.printStackTrace();
-    }
-  }
-
-
-
   public static void refreshVersionInfo(String dirName)
           throws URISyntaxException
   {
@@ -149,7 +102,8 @@ public class BioJsHTMLOutput extends HTMLOutput
       {
         try
         {
-          String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
+          String gitRepoPkgJson = getURLContentAsString(
+                  BJS_TEMPLATE_GIT_REPO);
           if (gitRepoPkgJson != null)
           {
             BioJSRepositoryPojo release = new BioJSRepositoryPojo(
@@ -251,8 +205,8 @@ public class BioJsHTMLOutput extends HTMLOutput
         }
       }
     }
-    return responseStrBuilder == null ? null : responseStrBuilder
-            .toString();
+    return responseStrBuilder == null ? null
+            : responseStrBuilder.toString();
   }
 
   public static File getCurrentBJSTemplateFile()
@@ -289,9 +243,37 @@ public class BioJsHTMLOutput extends HTMLOutput
   }
 
   @Override
-  public File getExportedFile()
+  public void run()
   {
-    return generatedFile;
+    try
+    {
+      String bioJSON = getBioJSONData();
+      String bioJSTemplateString = HTMLOutput
+              .readFileAsString(getCurrentBJSTemplateFile());
+      String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
+              .replaceAll("#sequenceData#", bioJSON).toString();
+
+      PrintWriter out = new java.io.PrintWriter(
+              new java.io.FileWriter(generatedFile));
+      out.print(generatedBioJsWithJalviewAlignmentAsJson);
+      out.flush();
+      out.close();
+      setProgressMessage(MessageManager
+              .formatMessage("status.export_complete", getDescription()));
+      exportCompleted();
+
+    } catch (OutOfMemoryError err)
+    {
+      System.out.println("########################\n" + "OUT OF MEMORY "
+              + generatedFile + "\n" + "########################");
+      new OOMWarning("Creating Image for " + generatedFile, err);
+    } catch (Exception e)
+    {
+      setProgressMessage(MessageManager
+              .formatMessage("info.error_creating_file", getDescription()));
+      e.printStackTrace();
+    }
+
   }
 
 }