Exporting plasmid maps with Java Plugin API

Sandra Peters

• August 13, 2019 21:32

What Geneious API classes are used to export a plasmid map from Geneious? From Geneious, I select a plasmid file, then go to File-> Save As Image File and am prompted for the format and dimensions of the image to save. I'd like to add this functionality to an existing Geneious Java Plugin. How is this done?

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• 

  Richard Moir

  • August 14, 2019 21:15

  Here's a method which you can hopefully adapt to your needs:

  /**
   * Export the sequence view of each document as a PNG image. NOTE: The sequence view will adopt whatever setting the user
   * has most recently used.
   *
   * @param documents documents to export
   * @param outputFolder folder to save PNGs in, each file will be named after the document: 'document.getName() + ".png"'
   * @param imageSize the resolution (in pixels) of the png file to export to, imageSize x imageSize (square)
   */
  static void batchExportSequenceViewAsPng(AnnotatedPluginDocument[] documents, File outputFolder, int imageSize) throws DocumentOperationException {
      outputFolder.mkdirs();
      for (AnnotatedPluginDocument doc : documents) {
          List<DocumentViewerFactory> documentViewerFactories = PluginUtilities.getDocumentViewerFactories(doc);
          for(DocumentViewerFactory factory : documentViewerFactories) {
              AtomicReference<DocumentOperationException> exception = new AtomicReference<>();
              String className = factory.getClass().getCanonicalName();
              if(className != null && className.equals("com.biomatters.plugins.sequenceviewer.SequenceViewerPlugin.SequenceViewerFactory")
                  && !factory.getName().contains("Annotation")) {
                  ThreadUtilities.invokeNowOrWait(() -> {
                      final DocumentViewer documentViewer = factory.createViewer(new AnnotatedPluginDocument[] {doc});
                      if (documentViewer == null) {
                          return;
                      }
                      JFrame dummyFrame = new JFrame();
                      dummyFrame.getContentPane().add(documentViewer.getComponent());
                      dummyFrame.pack();
                      ExtendedPrintable extendedPrintable = documentViewer.getExtendedPrintable();
                      if (extendedPrintable == null) {
                          return;
                      }
                      final BufferedImage image = new BufferedImage(imageSize, imageSize, BufferedImage.TYPE_INT_ARGB);
                      try {
                          Graphics2D g = image.createGraphics();
                          g.setClip(0,0, imageSize, imageSize);
                          Options options = extendedPrintable.getOptions(true);
                          options.setStringValue("printVisibleRegionOnly", "false");
                          extendedPrintable.print(g, new Dimension(imageSize, imageSize), 0, options);
                          g.dispose();
                      } catch (PrinterException e) {
                          exception.set(new DocumentOperationException(e));
                      }
                      try {
                          String fileName = FileUtilities.getLegalFileName(doc.getName(), " ");
                          ImageIO.write(image, "png", new File(outputFolder, fileName + ".png"));
                      } catch (IOException e) {
                          exception.set(new DocumentOperationException(e));
                      }
                      NoLongerViewedListener listener = documentViewer.getNoLongerViewedListener();
                      if(listener != null) {
                          listener.noLongerViewed(false);
                      }
                  });
              }
              if (exception.get() != null) {
                  throw exception.get();
              }
          }
      }
  }

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