src/jalview/io/BioJsHTMLOutput.java

   1 package jalview.io;
   2
   3 import static java.nio.file.Files.readAllBytes;
   4 import static java.nio.file.Paths.get;
   5 import jalview.datamodel.AlignmentI;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.gui.AlignViewport;
   8 import jalview.gui.AlignmentPanel;
   9 import jalview.gui.FeatureRenderer;
  10 import jalview.gui.SequenceRenderer;
  11 import jalview.util.MessageManager;
  12
  13 import java.io.IOException;
  14 import java.io.PrintWriter;
  15
  16 public class BioJsHTMLOutput
  17 {
  18   private AlignViewport av;
  19   private FeatureRenderer fr;
  20
  21   public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
  22           FeatureRenderer fr1)
  23   {
  24     System.out.println("BioJs working as expected so far");
  25     this.av = ap.av;
  26
  27     this.fr = new FeatureRenderer(ap);
  28     fr.transferSettings(fr1);
  29     exportAsBioJsHtml();
  30   }
  31
  32   private void exportAsBioJsHtml()
  33   {
  34     try
  35     {
  36       JalviewFileChooser jvFileChooser = getJalviewFileChooserOption();
  37       int fileChooserOpt = jvFileChooser.showSaveDialog(null);
  38       if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
  39       {
  40         jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
  41                 .getSelectedFile().getParent());
  42         String selectedFile = jvFileChooser.getSelectedFile().getPath();
  43         String generartedBioJs = generateBioJsAlignmentData(av
  44                 .getAlignment());
  45         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  46                 selectedFile));
  47         out.print(generartedBioJs);
  48         out.close();
  49         jalview.util.BrowserLauncher.openURL("file:///" + selectedFile);
  50       }
  51     } catch (Exception ex)
  52     {
  53       ex.printStackTrace();
  54     }
  55   }
  56
  57   private JalviewFileChooser getJalviewFileChooserOption()
  58   {
  59     JalviewFileChooser chooser = new JalviewFileChooser(
  60             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
  61             { "html" }, new String[]
  62             { "HTML files" }, "HTML files");
  63
  64     chooser.setFileView(new JalviewFileView());
  65     // TODO uncomment when supported by MassageManager
  66     // chooser.setDialogTitle(MessageManager.getString("label.save_as_biojs_html"));
  67     chooser.setDialogTitle("save as BioJs HTML");
  68     chooser.setToolTipText(MessageManager.getString("action.save"));
  69
  70     return chooser;
  71   }
  72
  73   private String generateBioJsAlignmentData(AlignmentI alignment)
  74           throws IOException
  75   {
  76     StringBuilder bioJsData = new StringBuilder();
  77     int count = 0;
  78     for (SequenceI seq : alignment.getSequences())
  79     {
  80       bioJsData.append("seqOnFly.push({seq:'" + seq.getSequenceAsString()
  81               + "', name:'" + seq.getName() + "', id:" + ++count + "});");
  82     }
  83     String bioJSTemplate = new String(
  84             readAllBytes(get("resources/templates/BioJSTemplate.txt")));
  85
  86     return bioJSTemplate.replaceAll("#sequenceData#", bioJsData.toString());
  87   }
  88
  89
  90 }
  91