JAL-1233 JAL-1576 copy constructor to propagate helix colours and applyTo implementat...

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

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 73be79f..50486f2 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,10 +1,11 @@
 package jalview.io;
 
+import jalview.api.AlignExportSettingI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
-import jalview.json.binding.v1.BioJSReleasePojo;
-import jalview.json.binding.v1.BioJSRepositoryPojo;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
 import jalview.util.MessageManager;
 
 import java.io.BufferedInputStream;
@@ -37,7 +38,7 @@ public class BioJsHTMLOutput
   public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
           .getDefault(
                   "biojs_template_git_repo",
-                  "https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
+                  "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
 
   public BioJsHTMLOutput(AlignmentViewPanel ap)
   {
@@ -53,9 +54,49 @@ public class BioJsHTMLOutput
     {
       String outputFile = getOutputFile();
       // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+      AlignExportSettingI exportSettings = new AlignExportSettingI()
+      {
+        @Override
+        public boolean isExportHiddenSequences()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportHiddenColumns()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportAnnotations()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportFeatures()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportGroups()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isCancelled()
+        {
+          return false;
+        }
+
+      };
       AlignmentExportData exportData = jalview.gui.AlignFrame
               .getAlignmentForExport(
-              JSONFile.FILE_DESC, ap.getAlignViewport());
+JSONFile.FILE_DESC,
+                      ap.getAlignViewport(), exportSettings);
       if (exportData.getSettings().isCancelled())
       {
         return;
@@ -98,7 +139,6 @@ public class BioJsHTMLOutput
 
     jvFileChooser.setDialogTitle(MessageManager
             .getString("label.save_as_biojs_html"));
-    jvFileChooser.setDialogTitle("save as BioJs HTML");
     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
 
     int fileChooserOpt = jvFileChooser.showSaveDialog(null);