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.json.binding.v1.BioJsAlignmentPojo;
  12 import jalview.json.binding.v1.BioJsSeqPojo;
  13 import jalview.util.MessageManager;
  14
  15 import java.io.IOException;
  16 import java.io.PrintWriter;
  17
  18 import org.jsoup.Jsoup;
  19 import org.jsoup.nodes.Document;
  20 import org.jsoup.nodes.Element;
  21
  22 import com.json.JSONException;
  23 import com.json.JSONObject;
  24
  25 public class BioJsHTMLOutput
  26 {
  27   private AlignViewport av;
  28   private FeatureRenderer fr;
  29
  30   public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
  31           FeatureRenderer fr1)
  32   {
  33     this.av = ap.av;
  34
  35     this.fr = new FeatureRenderer(ap);
  36     fr.transferSettings(fr1);
  37     exportAsBioJsHtml();
  38   }
  39
  40   private void exportAsBioJsHtml()
  41   {
  42     try
  43     {
  44       JalviewFileChooser jvFileChooser = getJalviewFileChooserOption();
  45       int fileChooserOpt = jvFileChooser.showSaveDialog(null);
  46       if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
  47       {
  48         jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
  49                 .getSelectedFile().getParent());
  50         String selectedFile = jvFileChooser.getSelectedFile().getPath();
  51         String generartedBioJs = generateBioJsAlignmentData(av
  52                 .getAlignment());
  53         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  54                 selectedFile));
  55         out.print(generartedBioJs);
  56         out.close();
  57         jalview.util.BrowserLauncher.openURL("file:///" + selectedFile);
  58       }
  59     } catch (Exception ex)
  60     {
  61       ex.printStackTrace();
  62     }
  63   }
  64
  65   private JalviewFileChooser getJalviewFileChooserOption()
  66   {
  67     JalviewFileChooser chooser = new JalviewFileChooser(
  68             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
  69             { "html" }, new String[]
  70             { "HTML files" }, "HTML files");
  71
  72     chooser.setFileView(new JalviewFileView());
  73     // TODO uncomment when supported by MassageManager
  74     // chooser.setDialogTitle(MessageManager.getString("label.save_as_biojs_html"));
  75     chooser.setDialogTitle("save as BioJs HTML");
  76     chooser.setToolTipText(MessageManager.getString("action.save"));
  77
  78     return chooser;
  79   }
  80
  81   private String generateBioJsAlignmentData(AlignmentI alignment)
  82           throws IOException, JSONException
  83   {
  84     BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
  85
  86     int count = 0;
  87     for (SequenceI seq : alignment.getSequences())
  88     {
  89       bjsAlignment.getSeqs().add(
  90               new BioJsSeqPojo(String.valueOf(++count), seq.getName(), seq
  91                       .getSequenceAsString()));
  92     }
  93
  94     String seqs = new JSONObject(bjsAlignment).getString("seqs");
  95     String bioJSTemplate = new String(
  96             readAllBytes(get("resources/templates/BioJSTemplate.txt")));
  97
  98     return bioJSTemplate.replaceAll("#sequenceData#", seqs);
  99   }
 100
 101   public static void main(String[] args) throws IOException
 102   {
 103     Document doc = Jsoup.parse(new String(
 104             readAllBytes(get("resources/templates/BioJSTemplate.txt"))));
 105
 106     Element content = doc.getElementById("seqData");
 107     System.out.println(content.val());
 108   }
 109
 110 }
 111