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;
import java.util.Objects;
import java.util.TreeMap;
-
public class BioJsHTMLOutput
{
private AlignmentViewPanel ap;
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());
+ .getAlignmentForExport(JSONFile.FILE_DESC,
+ ap.getAlignViewport(), exportSettings);
if (exportData.getSettings().isCancelled())
{
return;
String bioJSTemplateString = getBioJsTemplateAsString();
String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
- .replaceAll(
-"#sequenceData#", jalviewAlignmentJson)
+ .replaceAll("#sequenceData#", jalviewAlignmentJson)
.toString();
PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
{
String selectedFile = null;
JalviewFileChooser jvFileChooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "html" }, new String[]
- { "HTML files" }, "HTML files");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "html" }, new String[] { "HTML files" },
+ "HTML files");
jvFileChooser.setFileView(new JalviewFileView());
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);
return selectedFile;
}
-
- public static String getBioJsTemplateAsString()
- throws IOException
+ public static String getBioJsTemplateAsString() throws IOException
{
InputStreamReader isReader = null;
BufferedReader buffReader = null;
}
-
public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
{
for (BioJSReleasePojo bjsRelease : repo.getReleases())