+/*
+ * 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 jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentExportData;
import jalview.exceptions.NoFileSelectedException;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.OOMWarning;
import jalview.json.binding.biojs.BioJSReleasePojo;
import jalview.json.binding.biojs.BioJSRepositoryPojo;
import jalview.util.MessageManager;
import java.util.Objects;
import java.util.TreeMap;
-
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;
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)
+ 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"));
}
}
public void exportJalviewAlignmentAsBioJsHtmlFile()
{
+ String outputFile = null;
try
{
- String outputFile = getOutputFile();
- // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
- AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(
- JSONFile.FILE_DESC, ap.getAlignViewport());
- if (exportData.getSettings().isCancelled())
+ outputFile = getOutputFile();
+ AlignExportSettingI exportSettings = new AlignExportSettingI()
{
- return;
- }
- String jalviewAlignmentJson = new FormatAdapter(ap,
- exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
- exportData.getAlignment(), exportData.getOmitHidden(),
- exportData.getStartEndPostions(), ap.getAlignViewport()
- .getColumnSelection());
+ @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(), exportSettings);
+ 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));
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 (OutOfMemoryError err)
+ {
+ System.out.println("########################\n" + "OUT OF MEMORY "
+ + outputFile + "\n" + "########################");
+ new OOMWarning("Creating Image for " + outputFile, err);
} catch (Exception e)
{
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "info.error_creating_file", "HTML"), pSessionId);
e.printStackTrace();
}
}
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" }, "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);
}
else
{
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "BioJS"),
+ pSessionId);
throw new NoFileSelectedException("No file was selected.");
}
return selectedFile;
}
-
- public static String getBioJsTemplateAsString()
- throws IOException
+ public static String getBioJsTemplateAsString() throws IOException
{
InputStreamReader isReader = null;
BufferedReader buffReader = null;
{
Thread updateThread = new Thread()
{
+ @Override
public void run()
{
try
}
-
public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
{
for (BioJSReleasePojo bjsRelease : repo.getReleases())
git://source.jalview.org / jalview.git / blobdiff