X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=9454cae12b65f3adba5f5fead6759bd7e2430758;hb=c70d42a1afc972ddb3757b9ec4cece3458d396a1;hp=9b9be60964f1922504bbf94d14c7002014132df5;hpb=db4eacee27b836db4126dca551887bfc6652d72a;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 9b9be60..9454cae 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -24,6 +24,7 @@ import jalview.api.AlignExportSettingI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
+import jalview.gui.IProgressIndicator;
 import jalview.json.binding.biojs.BioJSReleasePojo;
 import jalview.json.binding.biojs.BioJSRepositoryPojo;
 import jalview.util.MessageManager;
@@ -44,6 +45,12 @@ 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;
@@ -59,11 +66,16 @@ 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"));
     }
   }
 
@@ -115,20 +127,15 @@ public class BioJsHTMLOutput
       AlignmentExportData exportData = jalview.gui.AlignFrame
               .getAlignmentForExport(JSONFile.FILE_DESC,
                       ap.getAlignViewport(), exportSettings);
-      if (exportData.getSettings().isCancelled())
-      {
-        return;
-      }
-      String jalviewAlignmentJson = new FormatAdapter(ap,
-              exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
-              exportData.getAlignment(), exportData.getOmitHidden(),
-              exportData.getStartEndPostions(), ap.getAlignViewport()
-                      .getColumnSelection());
+      String bioJSON = new FormatAdapter(ap, exportData.getSettings())
+              .formatSequences(JSONFile.FILE_DESC, exportData
+                      .getAlignment(), exportData.getOmitHidden(),
+                      exportData.getStartEndPostions(), ap
+                              .getAlignViewport().getColumnSelection());
 
       String bioJSTemplateString = getBioJsTemplateAsString();
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
-              .replaceAll("#sequenceData#", jalviewAlignmentJson)
-              .toString();
+              .replaceAll("#sequenceData#", bioJSON).toString();
 
       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
               outputFile));
@@ -136,11 +143,18 @@ 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 (Exception e)
     {
+      pIndicator.setProgressBar(MessageManager.formatMessage(
+              "info.error_creating_file", "HTML"), pSessionId);
       e.printStackTrace();
     }
   }
@@ -148,6 +162,13 @@ 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" },
@@ -167,6 +188,9 @@ public class BioJsHTMLOutput
     }
     else
     {
+      pIndicator.setProgressBar(MessageManager.formatMessage(
+              "status.cancelled_image_export_operation", "BioJS"),
+              pSessionId);
       throw new NoFileSelectedException("No file was selected.");
     }
     return selectedFile;
@@ -250,6 +274,7 @@ public class BioJsHTMLOutput
   {
     Thread updateThread = new Thread()
     {
+      @Override
       public void run()
       {
         try