src/jalview/io/BioJsHTMLOutput.java

   1 package jalview.io;
   2
   3 import jalview.datamodel.AlignmentI;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.gui.AlignViewport;
   6 import jalview.gui.AlignmentPanel;
   7 import jalview.gui.FeatureRenderer;
   8 import jalview.gui.SequenceRenderer;
   9 import jalview.json.binding.v1.BioJsAlignmentPojo;
  10 import jalview.json.binding.v1.BioJsSeqPojo;
  11 import jalview.util.MessageManager;
  12
  13 import java.io.BufferedReader;
  14 import java.io.IOException;
  15 import java.io.InputStreamReader;
  16 import java.io.PrintWriter;
  17 import java.net.URL;
  18
  19 import com.json.JSONException;
  20
  21 public class BioJsHTMLOutput
  22 {
  23   private AlignViewport av;
  24
  25   private FeatureRenderer fr;
  26
  27   public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
  28           FeatureRenderer fr1)
  29   {
  30     this.av = ap.av;
  31     this.fr = new FeatureRenderer(ap);
  32     fr.transferSettings(fr1);
  33     exportAsBioJsHtml();
  34   }
  35
  36   private void exportAsBioJsHtml()
  37   {
  38     try
  39     {
  40       JalviewFileChooser jvFileChooser = getJalviewFileChooserOption();
  41       int fileChooserOpt = jvFileChooser.showSaveDialog(null);
  42       if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
  43       {
  44         jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
  45                 .getSelectedFile().getParent());
  46         String selectedFile = jvFileChooser.getSelectedFile().getPath();
  47         String generartedBioJs = generateBioJsAlignmentData(av
  48                 .getAlignment());
  49         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  50                 selectedFile));
  51         out.print(generartedBioJs);
  52         out.close();
  53         jalview.util.BrowserLauncher.openURL("file:///" + selectedFile);
  54       }
  55     } catch (Exception ex)
  56     {
  57       ex.printStackTrace();
  58     }
  59   }
  60
  61   private JalviewFileChooser getJalviewFileChooserOption()
  62   {
  63     JalviewFileChooser chooser = new JalviewFileChooser(
  64             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
  65             { "html" }, new String[]
  66             { "HTML files" }, "HTML files");
  67     chooser.setFileView(new JalviewFileView());
  68
  69     // TODO uncomment when supported by MassageManager
  70     chooser.setDialogTitle(MessageManager
  71             .getString("label.save_as_biojs_html"));
  72     chooser.setDialogTitle("save as BioJs HTML");
  73     chooser.setToolTipText(MessageManager.getString("action.save"));
  74
  75     return chooser;
  76   }
  77
  78   private String generateBioJsAlignmentData(AlignmentI alignment)
  79           throws IOException, JSONException
  80   {
  81     BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
  82     int count = 0;
  83     for (SequenceI seq : alignment.getSequences())
  84     {
  85       StringBuilder name = new StringBuilder();
  86       name.append(seq.getName()).append("/").append(seq.getStart())
  87               .append("-").append(seq.getEnd());
  88       bjsAlignment.getSeqs().add(
  89               new BioJsSeqPojo(String.valueOf(++count), name.toString(),
  90                       seq.getSequenceAsString()));
  91     }
  92
  93     String seqs = new com.json.JSONObject(bjsAlignment).getString("seqs");
  94     // String bioJSTemplate = new String(
  95     // java.nio.file.Files.readAllBytes(java.nio.file.Paths
  96     // .get("resources/templates/BioJSTemplate.txt")));
  97     String bioJSTemplate = getBioJsTemplateAsString(alignment);
  98
  99     return bioJSTemplate.replaceAll("#sequenceData#", seqs).replaceAll(
 100             "#scheme#", "zappo");
 101   }
 102
 103
 104   public static String getBioJsTemplateAsString(AlignmentI bio)
 105           throws IOException
 106   {
 107      StringBuilder sb = new StringBuilder();
 108     URL url = bio.getClass().getResource(
 109             "/templates/BioJSTemplate.txt");
 110     if (url != null)
 111     {
 112       try
 113       {
 114         BufferedReader reader = new BufferedReader(new InputStreamReader(
 115                 url.openStream()));
 116         String line;
 117         String lineSeparator = System.getProperty("line.separator");
 118         while ((line = reader.readLine()) != null)
 119         {
 120           sb.append(line).append(lineSeparator);
 121         }
 122       } catch (Exception ex)
 123       {
 124         ex.printStackTrace();
 125       }
 126     }
 127
 128     return sb.toString();
 129   }
 130
 131 }