*/
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.AlignmentPanel;
import jalview.gui.OOMWarning;
import jalview.json.binding.biojs.BioJSReleasePojo;
import jalview.json.binding.biojs.BioJSRepositoryPojo;
import java.util.Objects;
import java.util.TreeMap;
-public class BioJsHTMLOutput
+public class BioJsHTMLOutput extends HTMLOutput
{
- private AlignmentViewPanel ap;
-
- private long pSessionId;
-
- private IProgressIndicator pIndicator;
-
- private boolean headless;
private static File currentBJSTemplateFile;
"biojs_template_git_repo",
"https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
- public BioJsHTMLOutput(AlignmentViewPanel ap,
- IProgressIndicator pIndicator)
+ public BioJsHTMLOutput(AlignmentPanel ap)
{
- 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"));
- }
+ super(ap);
}
- public void exportJalviewAlignmentAsBioJsHtmlFile()
+ @Override
+ public void exportHTML(String outputFile)
{
- String outputFile = null;
+ exportStarted();
try
{
- outputFile = getOutputFile();
- AlignExportSettingI exportSettings = new AlignExportSettingI()
+ if (outputFile == null)
{
- @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#", bioJSON).toString();
-
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
- outputFile));
- out.print(generatedBioJsWithJalviewAlignmentAsJson);
- out.flush();
- out.close();
- jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "status.export_complete", "BioJS"), pSessionId);
+ outputFile = getOutputFile();
}
- } catch (NoFileSelectedException ex)
+ generatedFile = new File(outputFile);
+ } catch (NoFileSelectedException e)
{
- // 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);
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "BioJS MSA"));
+ return;
} catch (Exception e)
{
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "info.error_creating_file", "HTML"), pSessionId);
+ setProgressMessage(MessageManager.formatMessage(
+ "info.error_creating_file", "BioJS MSA"));
e.printStackTrace();
+ return;
}
- }
-
- 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");
- jvFileChooser.setFileView(new JalviewFileView());
+ new Thread(this).start();
- jvFileChooser.setDialogTitle(MessageManager
- .getString("label.save_as_biojs_html"));
- jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
-
- int fileChooserOpt = jvFileChooser.showSaveDialog(null);
- if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
- {
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
- .getSelectedFile().getParent());
- selectedFile = jvFileChooser.getSelectedFile().getPath();
- }
- 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
- {
- InputStreamReader isReader = null;
- BufferedReader buffReader = null;
- StringBuilder sb = new StringBuilder();
- Objects.requireNonNull(getCurrentBJSTemplateFile(),
- "BioJsTemplate File not initialized!");
- @SuppressWarnings("deprecation")
- URL url = getCurrentBJSTemplateFile().toURL();
- if (url != null)
- {
- try
- {
- isReader = new InputStreamReader(url.openStream());
- buffReader = new BufferedReader(isReader);
- String line;
- String lineSeparator = System.getProperty("line.separator");
- while ((line = buffReader.readLine()) != null)
- {
- sb.append(line).append(lineSeparator);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (isReader != null)
- {
- isReader.close();
- }
- if (buffReader != null)
- {
- buffReader.close();
- }
- }
- }
- return sb.toString();
- }
-
- public static void refreshBioJSVersionsInfo(String dirName)
+ public static void refreshVersionInfo(String dirName)
throws URISyntaxException
{
File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
BioJSRepositoryPojo release = new BioJSRepositoryPojo(
gitRepoPkgJson);
syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
- refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
+ refreshVersionInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
}
} catch (URISyntaxException e)
{
BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
}
+ @Override
+ public boolean isEmbedData()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isLaunchInBrowserAfterExport()
+ {
+ return true;
+ }
+
+ @Override
+ public File getExportedFile()
+ {
+ return generatedFile;
+ }
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ String bioJSON = getBioJSONData();
+ String bioJSTemplateString = HTMLOutput
+ .readFileAsString(getCurrentBJSTemplateFile());
+ String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
+ .replaceAll("#sequenceData#", bioJSON).toString();
+
+ PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
+ generatedFile));
+ out.print(generatedBioJsWithJalviewAlignmentAsJson);
+ out.flush();
+ out.close();
+ setProgressMessage(MessageManager.formatMessage(
+ "status.export_complete", "BioJS"));
+ exportCompleted();
+
+ } catch (OutOfMemoryError err)
+ {
+ System.out.println("########################\n" + "OUT OF MEMORY "
+ + generatedFile + "\n" + "########################");
+ new OOMWarning("Creating Image for " + generatedFile, err);
+ } catch (Exception e)
+ {
+ setProgressMessage(MessageManager.formatMessage(
+ "info.error_creating_file", "HTML"));
+ e.printStackTrace();
+ }
+
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff