src/jalview/io/HtmlFile.java

   1 package jalview.io;
   2
   3 import jalview.datamodel.Sequence;
   4 import jalview.datamodel.SequenceFeature;
   5 import jalview.gui.AlignFrame;
   6 import jalview.json.binding.v1.BioJsAlignmentPojo.JalviewBioJsColorSchemeMapper;
   7 import jalview.schemes.ColourSchemeI;
   8
   9 import java.io.IOException;
  10 import java.util.Iterator;
  11
  12 import org.json.simple.JSONArray;
  13 import org.json.simple.JSONObject;
  14 import org.json.simple.parser.JSONParser;
  15 import org.jsoup.Jsoup;
  16 import org.jsoup.nodes.Document;
  17 import org.jsoup.nodes.Element;
  18
  19 public class HtmlFile extends AlignFile
  20 {
  21   public static final String FILE_EXT = "html";
  22
  23   public static final String FILE_DESC = "HTML";
  24
  25   private ColourSchemeI cs;
  26
  27   public HtmlFile()
  28   {
  29     super();
  30   }
  31
  32   public HtmlFile(FileParse source) throws IOException
  33   {
  34     super(source);
  35   }
  36
  37   public HtmlFile(String inFile, String type) throws IOException
  38   {
  39     super(inFile, type);
  40   }
  41
  42   @SuppressWarnings("unchecked")
  43   @Override
  44   public void parse() throws IOException
  45   {
  46     try
  47     {
  48       StringBuilder htmlData = new StringBuilder();
  49       String currentLine;
  50       while ((currentLine = nextLine()) != null)
  51       {
  52         htmlData.append(currentLine);
  53       }
  54
  55       Document doc = Jsoup.parse(htmlData.toString());
  56       Element content = doc.getElementById("seqData");
  57
  58       String alignmentJsonString = content.val();
  59       JSONParser jsonParser = new JSONParser();
  60       JSONObject alignmentJsonObj = (JSONObject) jsonParser
  61               .parse(alignmentJsonString);
  62       JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
  63       String bioJsColourScheme = (String) alignmentJsonObj
  64               .get("globalColorScheme");
  65       cs = getJalviewColorScheme(bioJsColourScheme);
  66
  67       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
  68               .hasNext();)
  69       {
  70         JSONObject sequence = sequenceIter.next();
  71         String sequcenceString = sequence.get("seq").toString();
  72         Sequence seq = new Sequence(sequence.get("name").toString(),
  73                 sequcenceString, 0, sequcenceString.length());
  74
  75         JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
  76         SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(jsonSeqArray);
  77         if (retrievedSeqFeatures != null)
  78         {
  79           seq.setSequenceFeatures(retrievedSeqFeatures);
  80         }
  81         seqs.add(seq);
  82
  83       }
  84     } catch (Exception e)
  85     {
  86       e.printStackTrace();
  87     }
  88   }
  89
  90   public SequenceFeature[] getJalviewSequenceFeatures(
  91           JSONArray jsonSeqFeatures)
  92   {
  93     SequenceFeature[] seqFeatures = null;
  94     int count = 0;
  95     if (jsonSeqFeatures != null)
  96     {
  97       seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
  98       for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
  99               .hasNext();)
 100       {
 101
 102         SequenceFeature sequenceFeature = new SequenceFeature();
 103         JSONObject jsonFeature = seqFeatureItr.next();
 104         Long begin = (Long) jsonFeature.get("xStart");
 105         Long end = (Long) jsonFeature.get("xEnd");
 106         String type = (String) jsonFeature.get("text");
 107
 108         String color = (String) jsonFeature.get("fillColor");
 109
 110         sequenceFeature.setBegin(begin.intValue());
 111         sequenceFeature.setEnd(end.intValue());
 112         sequenceFeature.setType(type);
 113         seqFeatures[count++] = sequenceFeature;
 114       }
 115     }
 116     return seqFeatures;
 117   }
 118
 119   public void LoadAlignmentFeatures(AlignFrame af)
 120   {
 121
 122     af.setShowSeqFeatures(true);
 123     af.changeColour(cs);
 124     af.setMenusForViewport();
 125   }
 126
 127   private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
 128   {
 129     ColourSchemeI jalviewColor = null;
 130     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
 131             .values())
 132     {
 133       if (cs.getBioJsName().equals(bioJsColourSchemeName))
 134       {
 135         jalviewColor = cs.getJvColourScheme();
 136         break;
 137       }
 138     }
 139     return jalviewColor;
 140   }
 141
 142   @Override
 143   public String print()
 144   {
 145     throw new UnsupportedOperationException(
 146             "Print method of HtmlFile not yet supported!");
 147   }
 148
 149 }