-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
package jalview.io;
import jalview.api.AlignExportSettingI;
import java.net.URL;
import java.util.Objects;
-
-public abstract class HTMLOutput
+public abstract class HTMLOutput implements Runnable
{
protected AlignmentPanel ap;
protected IProgressIndicator pIndicator;
- private boolean headless;
-
protected File generatedFile;
public HTMLOutput(AlignmentPanel ap)
}
}
-
public String getBioJSONData()
{
+ return getBioJSONData(null);
+ }
+
+ public String getBioJSONData(AlignExportSettingI exportSettings)
+ {
if (!isEmbedData())
{
return null;
}
- AlignExportSettingI exportSettings = new AlignExportSettingI()
+ if (exportSettings == null)
{
- @Override
- public boolean isExportHiddenSequences()
- {
- return true;
- }
-
- @Override
- public boolean isExportHiddenColumns()
+ exportSettings = new AlignExportSettingI()
{
- return true;
- }
+ @Override
+ public boolean isExportHiddenSequences()
+ {
+ return true;
+ }
- @Override
- public boolean isExportAnnotations()
- {
- return true;
- }
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return true;
+ }
- @Override
- public boolean isExportFeatures()
- {
- return true;
- }
+ @Override
+ public boolean isExportAnnotations()
+ {
+ return true;
+ }
- @Override
- public boolean isExportGroups()
- {
- return true;
- }
+ @Override
+ public boolean isExportFeatures()
+ {
+ return true;
+ }
- @Override
- public boolean isCancelled()
- {
- return false;
- }
+ @Override
+ public boolean isExportGroups()
+ {
+ return true;
+ }
- };
+ @Override
+ public boolean isCancelled()
+ {
+ return false;
+ }
+ };
+ }
AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(JSONFile.FILE_DESC,
+ .getAlignmentForExport(FileFormat.Json,
ap.getAlignViewport(), exportSettings);
String bioJSON = new FormatAdapter(ap, exportData.getSettings())
- .formatSequences(JSONFile.FILE_DESC, exportData.getAlignment(),
+ .formatSequences(FileFormat.Json, exportData.getAlignment(),
exportData.getOmitHidden(), exportData
- .getStartEndPostions(), ap.getAlignViewport()
- .getColumnSelection());
+.getStartEndPostions(), ap.getAlignViewport()
+ .getAlignment().getHiddenColumns());
return bioJSON;
}
public String getOutputFile() throws NoFileSelectedException
{
String selectedFile = null;
- if (pIndicator != null && !headless)
+ if (pIndicator != null && !isHeadless())
{
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" },
+ JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
"HTML files");
jvFileChooser.setFileView(new JalviewFileView());
jvFileChooser.setDialogTitle(MessageManager
- .getString("label.save_as_biojs_html"));
+ .getString("label.save_as_html"));
jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
int fileChooserOpt = jvFileChooser.showSaveDialog(null);
}
else
{
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "status.cancelled_image_export_operation", "BioJS"),
- pSessionId);
throw new NoFileSelectedException("No file was selected.");
}
return selectedFile;
protected void setProgressMessage(String message)
{
- if (pIndicator != null && !headless)
+ if (pIndicator != null && !isHeadless())
{
pIndicator.setProgressBar(message, pSessionId);
}
* the file path of the generated HTML
*/
public abstract void exportHTML(String outputFile);
-}
+}
\ No newline at end of file