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;
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)
{
{
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;
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);