src/jalview/io/BioJsHTMLOutput.java

   1 package jalview.io;
   2
   3 import jalview.api.FeaturesDisplayedI;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.SequenceFeature;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.exceptions.NoFileSelectedException;
   8 import jalview.gui.AlignViewport;
   9 import jalview.gui.AlignmentPanel;
  10 import jalview.gui.FeatureRenderer;
  11 import jalview.json.binding.v1.BioJsAlignmentPojo;
  12 import jalview.json.binding.v1.BioJsFeaturePojo;
  13 import jalview.json.binding.v1.BioJsSeqPojo;
  14 import jalview.schemes.ColourSchemeProperty;
  15 import jalview.util.MessageManager;
  16
  17 import java.awt.Color;
  18 import java.io.BufferedReader;
  19 import java.io.IOException;
  20 import java.io.InputStreamReader;
  21 import java.io.PrintWriter;
  22 import java.net.URL;
  23 import java.util.ArrayList;
  24
  25 import com.json.JSONException;
  26
  27 public class BioJsHTMLOutput
  28 {
  29   private AlignViewport av;
  30
  31   private jalview.api.FeatureRenderer fr;
  32
  33   private String globalColorScheme;
  34
  35   private FeaturesDisplayedI displayedFeatures;
  36
  37   private String jalviewVersion;
  38
  39   private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
  40
  41   public BioJsHTMLOutput(AlignmentPanel ap,
  42           FeatureRenderer fr1)
  43   {
  44
  45     jalviewVersion = jalview.bin.Cache.getProperty("VERSION");
  46     webStartLaunchServletUrl = jalview.bin.Cache.getDefault(
  47             "www.jalview.org", "http://www.jalview.org")
  48             + "/services/launchApp";
  49     if (ap != null)
  50     {
  51       this.av = ap.av;
  52       this.globalColorScheme = ColourSchemeProperty.getColourName(av
  53               .getGlobalColourScheme());
  54       this.fr = ap.cloneFeatureRenderer();
  55       displayedFeatures = av.getFeaturesDisplayed();
  56     }
  57   }
  58
  59   private void exportJalviewAlignmentAsBioJsHtmlFile()
  60   {
  61     try
  62     {
  63       String outputFile = getOutputFile();
  64       String jalviewAlignmentJson = getJalviewAlignmentAsJsonString(av
  65               .getAlignment());
  66       String bioJSTemplateString = getBioJsTemplateAsString(this);
  67       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
  68               .replaceAll(
  69 "#sequenceData#", jalviewAlignmentJson)
  70               .toString();
  71
  72       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
  73               outputFile));
  74       out.print(generatedBioJsWithJalviewAlignmentAsJson);
  75       out.flush();
  76       out.close();
  77       jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
  78     } catch (NoFileSelectedException ex)
  79     {
  80       // do noting if no file was selected
  81     } catch (Exception e)
  82     {
  83       e.printStackTrace();
  84     }
  85   }
  86
  87   public String getOutputFile() throws NoFileSelectedException
  88   {
  89     String selectedFile = null;
  90     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
  91             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
  92             { "html" }, new String[]
  93             { "HTML files" }, "HTML files");
  94     jvFileChooser.setFileView(new JalviewFileView());
  95
  96     // TODO uncomment when supported by MassageManager
  97     jvFileChooser.setDialogTitle(MessageManager
  98             .getString("label.save_as_biojs_html"));
  99     jvFileChooser.setDialogTitle("save as BioJs HTML");
 100     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
 101
 102     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
 103     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
 104     {
 105       jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
 106               .getSelectedFile().getParent());
 107       selectedFile = jvFileChooser.getSelectedFile().getPath();
 108     }
 109     else
 110     {
 111       throw new NoFileSelectedException("No file was selected.");
 112     }
 113
 114     return selectedFile;
 115   }
 116
 117   public String getJalviewAlignmentAsJsonString(AlignmentI alignment)
 118           throws IOException, JSONException
 119   {
 120     BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
 121
 122     bjsAlignment.setGlobalColorScheme(getGlobalColorScheme());
 123     bjsAlignment.setJalviewVersion(jalviewVersion);
 124     bjsAlignment.setWebStartUrl(webStartLaunchServletUrl);
 125
 126     int count = 0;
 127     for (SequenceI seq : alignment.getSequences())
 128     {
 129       StringBuilder name = new StringBuilder();
 130       name.append(seq.getName()).append("/").append(seq.getStart())
 131               .append("-").append(seq.getEnd());
 132
 133       BioJsSeqPojo seqPojo = new BioJsSeqPojo();
 134       seqPojo.setId(String.valueOf(++count));
 135       seqPojo.setEnd(seq.getEnd());
 136       seqPojo.setStart(seq.getStart());
 137       seqPojo.setName(name.toString());
 138       seqPojo.setSeq(seq.getSequenceAsString());
 139
 140       SequenceFeature[] seqFeatures = seq.getDatasetSequence()
 141               .getSequenceFeatures();
 142       if (seqFeatures != null)
 143       {
 144         ArrayList<BioJsFeaturePojo> bjsSeqFeatures = new ArrayList<BioJsFeaturePojo>();
 145         for (SequenceFeature sf : seqFeatures)
 146         {
 147           if (displayedFeatures != null
 148                   && displayedFeatures.isVisible(sf.getType()))
 149           {
 150
 151             // TODO: translate graduated/complex colourschemes to biojs model
 152             String featureColour = jalview.util.Format.getHexString(fr
 153                     .findFeatureColour(Color.white, seq,
 154                             seq.findIndex(sf.getBegin())));
 155             BioJsFeaturePojo bjsFeature = new BioJsFeaturePojo();
 156             bjsFeature.setFillColor(featureColour);
 157             bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
 158             bjsFeature.setXend(seq.findIndex(sf.getEnd()));
 159             bjsFeature.setText(sf.getType());
 160             bjsSeqFeatures.add(bjsFeature);
 161           }
 162         }
 163         seqPojo.setFeatures(bjsSeqFeatures);
 164       }
 165       bjsAlignment.getSeqs().add(seqPojo);
 166     }
 167
 168     return new com.json.JSONObject(bjsAlignment).toString()
 169             .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd");
 170   }
 171
 172   public static String getBioJsTemplateAsString(Object currentObj)
 173           throws IOException
 174   {
 175     InputStreamReader isReader = null;
 176     BufferedReader buffReader = null;
 177     StringBuilder sb = new StringBuilder();
 178     URL url = currentObj.getClass().getResource(
 179             "/templates/BioJSTemplate.txt");
 180     if (url != null)
 181     {
 182       try
 183       {
 184         isReader = new InputStreamReader(url.openStream());
 185         buffReader = new BufferedReader(isReader);
 186         String line;
 187         String lineSeparator = System.getProperty("line.separator");
 188         while ((line = buffReader.readLine()) != null)
 189         {
 190           sb.append(line).append(lineSeparator);
 191         }
 192
 193       } catch (Exception ex)
 194       {
 195         ex.printStackTrace();
 196       } finally
 197       {
 198         if (isReader != null)
 199         {
 200           isReader.close();
 201         }
 202
 203         if (buffReader != null)
 204         {
 205           buffReader.close();
 206         }
 207       }
 208     }
 209     return sb.toString();
 210   }
 211
 212   public String getGlobalColorScheme()
 213   {
 214     return globalColorScheme;
 215   }
 216
 217   public void setGlobalColorScheme(String globalColorScheme)
 218   {
 219     this.globalColorScheme = globalColorScheme;
 220   }
 221
 222 }