src/jalview/io/BioJsHTMLOutput.java

   1 package jalview.io;
   2
   3 import jalview.exceptions.NoFileSelectedException;
   4 import jalview.gui.AlignViewport;
   5 import jalview.gui.AlignmentPanel;
   6 import jalview.gui.FeatureRenderer;
   7 import jalview.util.MessageManager;
   8
   9 import java.io.BufferedReader;
  10 import java.io.IOException;
  11 import java.io.InputStreamReader;
  12 import java.io.PrintWriter;
  13 import java.net.URL;
  14
  15 public class BioJsHTMLOutput
  16 {
  17   private AlignViewport av;
  18
  19
  20   public BioJsHTMLOutput(AlignmentPanel ap,
  21           FeatureRenderer fr1)
  22   {
  23
  24     if (ap != null)
  25     {
  26
  27       this.av = ap.av;
  28       av.setFeatureRenderer(new FeatureRenderer(ap));
  29     }
  30     exportJalviewAlignmentAsBioJsHtmlFile();
  31   }
  32
  33   private void exportJalviewAlignmentAsBioJsHtmlFile()
  34   {
  35     try
  36     {
  37       String outputFile = getOutputFile();
  38       String jalviewAlignmentJson = JSONFile.getJSONData(av);
  39       String bioJSTemplateString = getBioJsTemplateAsString(this);
  40       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
  41               .replaceAll(
  42 "#sequenceData#", jalviewAlignmentJson)
  43               .toString();
  44
  45       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  46               outputFile));
  47       out.print(generatedBioJsWithJalviewAlignmentAsJson);
  48       out.flush();
  49       out.close();
  50       jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
  51     } catch (NoFileSelectedException ex)
  52     {
  53       // do noting if no file was selected
  54     } catch (Exception e)
  55     {
  56       e.printStackTrace();
  57     }
  58   }
  59
  60   public String getOutputFile() throws NoFileSelectedException
  61   {
  62     String selectedFile = null;
  63     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
  64             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
  65             { "html" }, new String[]
  66             { "HTML files" }, "HTML files");
  67     jvFileChooser.setFileView(new JalviewFileView());
  68
  69     // TODO uncomment when supported by MassageManager
  70     jvFileChooser.setDialogTitle(MessageManager
  71             .getString("label.save_as_biojs_html"));
  72     jvFileChooser.setDialogTitle("save as BioJs HTML");
  73     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
  74
  75     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
  76     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
  77     {
  78       jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
  79               .getSelectedFile().getParent());
  80       selectedFile = jvFileChooser.getSelectedFile().getPath();
  81     }
  82     else
  83     {
  84       throw new NoFileSelectedException("No file was selected.");
  85     }
  86     return selectedFile;
  87   }
  88
  89
  90   public static String getBioJsTemplateAsString(Object currentObj)
  91           throws IOException
  92   {
  93     InputStreamReader isReader = null;
  94     BufferedReader buffReader = null;
  95     StringBuilder sb = new StringBuilder();
  96     URL url = currentObj.getClass().getResource(
  97             "/templates/BioJSTemplate.txt");
  98     if (url != null)
  99     {
 100       try
 101       {
 102         isReader = new InputStreamReader(url.openStream());
 103         buffReader = new BufferedReader(isReader);
 104         String line;
 105         String lineSeparator = System.getProperty("line.separator");
 106         while ((line = buffReader.readLine()) != null)
 107         {
 108           sb.append(line).append(lineSeparator);
 109         }
 110
 111       } catch (Exception ex)
 112       {
 113         ex.printStackTrace();
 114       } finally
 115       {
 116         if (isReader != null)
 117         {
 118           isReader.close();
 119         }
 120
 121         if (buffReader != null)
 122         {
 123           buffReader.close();
 124         }
 125       }
 126     }
 127     return sb.toString();
 128   }
 129 }