src/jalview/io/BioJsHTMLOutput.java

   1 package jalview.io;
   2
   3 import jalview.datamodel.AlignmentI;
   4 import jalview.datamodel.SequenceFeature;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.gui.AlignViewport;
   7 import jalview.gui.AlignmentPanel;
   8 import jalview.gui.FeatureRenderer;
   9 import jalview.gui.SequenceRenderer;
  10 import jalview.json.binding.v1.BioJsAlignmentPojo;
  11 import jalview.json.binding.v1.BioJsFeaturePojo;
  12 import jalview.json.binding.v1.BioJsSeqPojo;
  13 import jalview.schemes.ColourSchemeProperty;
  14 import jalview.util.MessageManager;
  15
  16 import java.io.BufferedReader;
  17 import java.io.IOException;
  18 import java.io.InputStreamReader;
  19 import java.io.PrintWriter;
  20 import java.net.URL;
  21 import java.util.ArrayList;
  22
  23 import com.json.JSONException;
  24
  25 public class BioJsHTMLOutput
  26 {
  27   private AlignViewport av;
  28
  29   private FeatureRenderer fr;
  30
  31   public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
  32           FeatureRenderer fr1)
  33   {
  34     this.av = ap.av;
  35     this.fr = new FeatureRenderer(ap);
  36     fr.transferSettings(fr1);
  37
  38     exportAsBioJsHtml();
  39   }
  40
  41   private void exportAsBioJsHtml()
  42   {
  43     try
  44     {
  45       JalviewFileChooser jvFileChooser = getJalviewFileChooserOption();
  46       int fileChooserOpt = jvFileChooser.showSaveDialog(null);
  47       if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
  48       {
  49         jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
  50                 .getSelectedFile().getParent());
  51         String selectedFile = jvFileChooser.getSelectedFile().getPath();
  52         String generartedBioJs = generateBioJsAlignmentData(av
  53                 .getAlignment());
  54         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  55                 selectedFile));
  56         out.print(generartedBioJs);
  57         out.close();
  58         jalview.util.BrowserLauncher.openURL("file:///" + selectedFile);
  59       }
  60     } catch (Exception ex)
  61     {
  62       ex.printStackTrace();
  63     }
  64   }
  65
  66   private JalviewFileChooser getJalviewFileChooserOption()
  67   {
  68     JalviewFileChooser chooser = new JalviewFileChooser(
  69             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
  70             { "html" }, new String[]
  71             { "HTML files" }, "HTML files");
  72     chooser.setFileView(new JalviewFileView());
  73
  74     // TODO uncomment when supported by MassageManager
  75     chooser.setDialogTitle(MessageManager
  76             .getString("label.save_as_biojs_html"));
  77     chooser.setDialogTitle("save as BioJs HTML");
  78     chooser.setToolTipText(MessageManager.getString("action.save"));
  79
  80     return chooser;
  81   }
  82
  83   private String generateBioJsAlignmentData(AlignmentI alignment)
  84           throws IOException, JSONException
  85   {
  86     BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
  87     bjsAlignment.setGlobalColorScheme(ColourSchemeProperty.getColourName(av
  88             .getGlobalColourScheme()));
  89
  90     // av.setGlobalColourScheme(cs);
  91     int count = 0;
  92     for (SequenceI seq : alignment.getSequences())
  93     {
  94       StringBuilder name = new StringBuilder();
  95       name.append(seq.getName()).append("/").append(seq.getStart())
  96               .append("-").append(seq.getEnd());
  97       // BioJsSeqPojo seqPojo = new BioJsSeqPojo(seq.getStart(), seq.getEnd(),
  98       // String.valueOf(++count),
  99       // name.toString(), seq.getSequenceAsString());
 100       //
 101       BioJsSeqPojo seqPojo = new BioJsSeqPojo();
 102       seqPojo.setId(String.valueOf(++count));
 103       seqPojo.setEnd(seq.getEnd());
 104       seqPojo.setStart(seq.getStart());
 105       seqPojo.setName(name.toString());
 106       seqPojo.setSeq(seq.getSequenceAsString());
 107
 108       SequenceFeature[] seqFeatures = seq.getDatasetSequence()
 109               .getSequenceFeatures();
 110       if (seqFeatures != null)
 111       {
 112
 113         ArrayList<BioJsFeaturePojo> bjsSeqFeatures = new ArrayList<BioJsFeaturePojo>();
 114         for (SequenceFeature sf : seqFeatures)
 115         {
 116
 117           String featureColour = jalview.util.Format.getHexString(fr
 118                   .getColour(sf));
 119           BioJsFeaturePojo bjsFeature = new BioJsFeaturePojo();
 120           bjsFeature.setFillColor(featureColour);
 121           bjsFeature.setXstart(sf.getBegin());
 122           bjsFeature.setXend(sf.getEnd());
 123           bjsFeature.setText(sf.getType());
 124
 125           bjsSeqFeatures.add(bjsFeature);
 126
 127         }
 128
 129         seqPojo.setFeatures(bjsSeqFeatures);
 130       }
 131       bjsAlignment.getSeqs().add(seqPojo);
 132     }
 133
 134     String jalviewData = new com.json.JSONObject(bjsAlignment).toString()
 135             .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd");
 136     // String bioJSTemplate = new String(
 137     // java.nio.file.Files.readAllBytes(java.nio.file.Paths
 138     // .get("resources/templates/BioJSTemplate.txt")));
 139     String bioJSTemplate = getBioJsTemplateAsString(this);
 140
 141     return bioJSTemplate.replaceAll("#sequenceData#", jalviewData)
 142             .replaceAll(
 143                     "#jalview_logo#",
 144                     alignment.getClass()
 145                             .getResource("/images/Jalview_Logo.png")
 146                             .toString());
 147   }
 148
 149   public static String getBioJsTemplateAsString(Object currentObj)
 150           throws IOException
 151   {
 152     InputStreamReader isReader = null;
 153     BufferedReader buffReader = null;
 154     StringBuilder sb = new StringBuilder();
 155     URL url = currentObj.getClass().getResource(
 156             "/templates/BioJSTemplate.txt");
 157     if (url != null)
 158     {
 159       try
 160       {
 161         isReader = new InputStreamReader(url.openStream());
 162         buffReader = new BufferedReader(isReader);
 163         String line;
 164         String lineSeparator = System.getProperty("line.separator");
 165         while ((line = buffReader.readLine()) != null)
 166         {
 167           sb.append(line).append(lineSeparator);
 168         }
 169
 170       } catch (Exception ex)
 171       {
 172         ex.printStackTrace();
 173       } finally
 174       {
 175         if (isReader != null)
 176         {
 177           isReader.close();
 178         }
 179
 180         if (buffReader != null)
 181         {
 182           buffReader.close();
 183         }
 184       }
 185     }
 186
 187     return sb.toString();
 188   }
 189
 190 }