JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 47f285c..f8fa1f5 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -24,6 +24,8 @@ import jalview.api.AlignExportSettingI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.OOMWarning;
 import jalview.json.binding.biojs.BioJSReleasePojo;
 import jalview.json.binding.biojs.BioJSRepositoryPojo;
 import jalview.util.MessageManager;
@@ -44,6 +46,12 @@ public class BioJsHTMLOutput
 {
   private AlignmentViewPanel ap;
 
+  private long pSessionId;
+
+  private IProgressIndicator pIndicator;
+
+  private boolean headless;
+
   private static File currentBJSTemplateFile;
 
   private static TreeMap<String, File> bioJsMSAVersions;
@@ -59,20 +67,25 @@ public class BioJsHTMLOutput
                   "biojs_template_git_repo",
                   "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
 
-  public BioJsHTMLOutput(AlignmentViewPanel ap)
+  public BioJsHTMLOutput(AlignmentViewPanel ap,
+          IProgressIndicator pIndicator)
   {
     if (ap != null)
     {
       this.ap = ap;
+      this.pSessionId = System.currentTimeMillis();
+      this.pIndicator = pIndicator;
+      this.headless = (System.getProperty("java.awt.headless") != null && System
+              .getProperty("java.awt.headless").equals("true"));
     }
   }
 
   public void exportJalviewAlignmentAsBioJsHtmlFile()
   {
+    String outputFile = null;
     try
     {
-      String outputFile = getOutputFile();
-      // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+      outputFile = getOutputFile();
       AlignExportSettingI exportSettings = new AlignExportSettingI()
       {
         @Override
@@ -131,11 +144,23 @@ public class BioJsHTMLOutput
       out.flush();
       out.close();
       jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
+      if (pIndicator != null && !headless)
+      {
+        pIndicator.setProgressBar(MessageManager.formatMessage(
+                "status.export_complete", "BioJS"), pSessionId);
+      }
     } 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)
     {
+      pIndicator.setProgressBar(MessageManager.formatMessage(
+              "info.error_creating_file", "HTML"), pSessionId);
       e.printStackTrace();
     }
   }
@@ -143,6 +168,13 @@ public class BioJsHTMLOutput
   public String getOutputFile() throws NoFileSelectedException
   {
     String selectedFile = null;
+    if (pIndicator != null && !headless)
+    {
+      pIndicator.setProgressBar(MessageManager.formatMessage(
+              "status.waiting_for_user_to_select_output_file", "HTML"),
+              pSessionId);
+    }
+
     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
             new String[] { "html" }, new String[] { "HTML files" },
@@ -162,6 +194,9 @@ public class BioJsHTMLOutput
     }
     else
     {
+      pIndicator.setProgressBar(MessageManager.formatMessage(
+              "status.cancelled_image_export_operation", "BioJS"),
+              pSessionId);
       throw new NoFileSelectedException("No file was selected.");
     }
     return selectedFile;
@@ -245,6 +280,7 @@ public class BioJsHTMLOutput
   {
     Thread updateThread = new Thread()
     {
+      @Override
       public void run()
       {
         try