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.exceptions.NoFileSelectedException;
   7 import jalview.gui.AlignViewport;
   8 import jalview.gui.AlignmentPanel;
   9 import jalview.gui.FeatureRenderer;
  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 import java.util.Hashtable;
  23
  24 import com.json.JSONException;
  25
  26 public class BioJsHTMLOutput
  27 {
  28   private AlignViewport av;
  29
  30   private FeatureRenderer fr;
  31
  32   private String globalColorScheme;
  33
  34   private Hashtable displayedFeatures;
  35
  36   private String jalviewVersion;
  37
  38   private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
  39
  40   public BioJsHTMLOutput(AlignmentPanel ap,
  41           FeatureRenderer fr1)
  42   {
  43
  44     jalviewVersion = jalview.bin.Cache.getProperty("VERSION");
  45     webStartLaunchServletUrl = jalview.bin.Cache.getDefault(
  46             "www.jalview.org", "http://www.jalview.org")
  47             + "/services/launchApp";
  48     if (ap != null)
  49     {
  50       this.av = ap.av;
  51       this.globalColorScheme = ColourSchemeProperty.getColourName(av
  52               .getGlobalColourScheme());
  53       this.fr = new FeatureRenderer(ap);
  54     fr.transferSettings(fr1);
  55       displayedFeatures = av.getFeaturesDisplayed();
  56
  57     exportJalviewAlignmentAsBioJsHtmlFile();
  58   }
  59   }
  60
  61   private void exportJalviewAlignmentAsBioJsHtmlFile()
  62   {
  63     try
  64     {
  65       String outputFile = getOutputFile();
  66       String jalviewAlignmentJson = getJalviewAlignmentAsJsonString(av
  67               .getAlignment());
  68       String bioJSTemplateString = getBioJsTemplateAsString(this);
  69       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
  70               .replaceAll(
  71 "#sequenceData#", jalviewAlignmentJson)
  72               .toString();
  73
  74       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  75               outputFile));
  76       out.print(generatedBioJsWithJalviewAlignmentAsJson);
  77       out.flush();
  78       out.close();
  79       jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
  80     } catch (NoFileSelectedException ex)
  81     {
  82       // do noting if no file was selected
  83     } catch (Exception e)
  84     {
  85       e.printStackTrace();
  86     }
  87   }
  88
  89   public String getOutputFile() throws NoFileSelectedException
  90   {
  91     String selectedFile = null;
  92     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
  93             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
  94             { "html" }, new String[]
  95             { "HTML files" }, "HTML files");
  96     jvFileChooser.setFileView(new JalviewFileView());
  97
  98     // TODO uncomment when supported by MassageManager
  99     jvFileChooser.setDialogTitle(MessageManager
 100             .getString("label.save_as_biojs_html"));
 101     jvFileChooser.setDialogTitle("save as BioJs HTML");
 102     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
 103
 104     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
 105     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
 106     {
 107       jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
 108               .getSelectedFile().getParent());
 109       selectedFile = jvFileChooser.getSelectedFile().getPath();
 110     }
 111     else
 112     {
 113       throw new NoFileSelectedException("No file was selected.");
 114     }
 115
 116     return selectedFile;
 117   }
 118
 119   public String getJalviewAlignmentAsJsonString(AlignmentI alignment)
 120           throws IOException, JSONException
 121   {
 122     BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
 123
 124     bjsAlignment.setGlobalColorScheme(getGlobalColorScheme());
 125     bjsAlignment.setJalviewVersion(jalviewVersion);
 126     bjsAlignment.setWebStartUrl(webStartLaunchServletUrl);
 127
 128     int count = 0;
 129     for (SequenceI seq : alignment.getSequences())
 130     {
 131       StringBuilder name = new StringBuilder();
 132       name.append(seq.getName()).append("/").append(seq.getStart())
 133               .append("-").append(seq.getEnd());
 134
 135       BioJsSeqPojo seqPojo = new BioJsSeqPojo();
 136       seqPojo.setId(String.valueOf(++count));
 137       seqPojo.setEnd(seq.getEnd());
 138       seqPojo.setStart(seq.getStart());
 139       seqPojo.setName(name.toString());
 140       seqPojo.setSeq(seq.getSequenceAsString());
 141
 142       SequenceFeature[] seqFeatures = seq.getDatasetSequence()
 143               .getSequenceFeatures();
 144       if (seqFeatures != null)
 145       {
 146         ArrayList<BioJsFeaturePojo> bjsSeqFeatures = new ArrayList<BioJsFeaturePojo>();
 147         for (SequenceFeature sf : seqFeatures)
 148         {
 149           if (displayedFeatures != null
 150                   && displayedFeatures.get(sf.getType()) != null)
 151           {
 152             String featureColour = jalview.util.Format.getHexString(fr
 153                     .getColour(sf));
 154             BioJsFeaturePojo bjsFeature = new BioJsFeaturePojo();
 155             bjsFeature.setFillColor(featureColour);
 156             bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 157             bjsFeature.setXend(seq.findIndex(sf.getEnd()));
 158             bjsFeature.setText(sf.getType());
 159             bjsSeqFeatures.add(bjsFeature);
 160           }
 161         }
 162         seqPojo.setFeatures(bjsSeqFeatures);
 163       }
 164       bjsAlignment.getSeqs().add(seqPojo);
 165     }
 166
 167     return new com.json.JSONObject(bjsAlignment).toString()
 168             .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd");
 169   }
 170
 171   public static String getBioJsTemplateAsString(Object currentObj)
 172           throws IOException
 173   {
 174     InputStreamReader isReader = null;
 175     BufferedReader buffReader = null;
 176     StringBuilder sb = new StringBuilder();
 177     URL url = currentObj.getClass().getResource(
 178             "/templates/BioJSTemplate.txt");
 179     if (url != null)
 180     {
 181       try
 182       {
 183         isReader = new InputStreamReader(url.openStream());
 184         buffReader = new BufferedReader(isReader);
 185         String line;
 186         String lineSeparator = System.getProperty("line.separator");
 187         while ((line = buffReader.readLine()) != null)
 188         {
 189           sb.append(line).append(lineSeparator);
 190         }
 191
 192       } catch (Exception ex)
 193       {
 194         ex.printStackTrace();
 195       } finally
 196       {
 197         if (isReader != null)
 198         {
 199           isReader.close();
 200         }
 201
 202         if (buffReader != null)
 203         {
 204           buffReader.close();
 205         }
 206       }
 207     }
 208     return sb.toString();
 209   }
 210
 211   public String getGlobalColorScheme()
 212   {
 213     return globalColorScheme;
 214   }
 215
 216   public void setGlobalColorScheme(String globalColorScheme)
 217   {
 218     this.globalColorScheme = globalColorScheme;
 219   }
 220
 221 }