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.json.simple.parser.ParseException;
  19
  20 import com.json.JSONException;
  21
  22 public class BioJsHTMLOutput {
  23         private AlignViewport av;
  24         private FeatureRenderer fr;
  25
  26         public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1) {
  27                 this.av = ap.av;
  28                 this.fr = new FeatureRenderer(ap);
  29                 fr.transferSettings(fr1);
  30                 exportAsBioJsHtml();
  31         }
  32
  33         private void exportAsBioJsHtml() {
  34                 try {
  35                         JalviewFileChooser jvFileChooser = getJalviewFileChooserOption();
  36                         int fileChooserOpt = jvFileChooser.showSaveDialog(null);
  37                         if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION) {
  38                                 jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser.getSelectedFile().getParent());
  39                                 String selectedFile = jvFileChooser.getSelectedFile().getPath();
  40                                 String generartedBioJs = generateBioJsAlignmentData(av.getAlignment());
  41                                 PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(selectedFile));
  42                                 out.print(generartedBioJs);
  43                                 out.close();
  44                                 jalview.util.BrowserLauncher.openURL("file:///" + selectedFile);
  45                         }
  46                 } catch (Exception ex) {
  47                         ex.printStackTrace();
  48                 }
  49         }
  50
  51         private JalviewFileChooser getJalviewFileChooserOption() {
  52                 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { "html" }, new String[] { "HTML files" }, "HTML files");
  53                 chooser.setFileView(new JalviewFileView());
  54
  55                 // TODO uncomment when supported by MassageManager
  56                 chooser.setDialogTitle(MessageManager.getString("label.save_as_biojs_html"));
  57                 chooser.setDialogTitle("save as BioJs HTML");
  58                 chooser.setToolTipText(MessageManager.getString("action.save"));
  59
  60                 return chooser;
  61         }
  62
  63         private String generateBioJsAlignmentData(AlignmentI alignment) throws IOException, JSONException {
  64                 BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
  65                 int count = 0;
  66                 for (SequenceI seq : alignment.getSequences()) {
  67                         StringBuilder name = new StringBuilder();
  68                         name.append(seq.getName()).append("/").append(seq.getStart()).append("-").append(seq.getEnd());
  69                         bjsAlignment.getSeqs().add(new BioJsSeqPojo(String.valueOf(++count), name.toString(), seq.getSequenceAsString()));
  70                 }
  71
  72                 // Taylor
  73                 // av.getGlobalColourScheme().;
  74                 String seqs = new com.json.JSONObject(bjsAlignment).getString("seqs");
  75                 String bioJSTemplate = new String(readAllBytes(get("resources/templates/BioJSTemplate.txt")));
  76
  77                 // av.get
  78                 // fr.
  79                 return bioJSTemplate.replaceAll("#sequenceData#", seqs).replaceAll("#scheme#", "zappo");
  80         }
  81
  82         public static void main(String[] args) throws IOException, ParseException {
  83
  84         }
  85
  86 }