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, Integer.valueOf(sequence.get("start")
  74                         .toString()), Integer.valueOf(sequence.get("end")
  75                         .toString()));
  76
  77         JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
  78         SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
  79                 jsonSeqArray, seq);
  80         if (retrievedSeqFeatures != null)
  81         {
  82           seq.setSequenceFeatures(retrievedSeqFeatures);
  83         }
  84         seqs.add(seq);
  85
  86       }
  87     } catch (Exception e)
  88     {
  89       e.printStackTrace();
  90     }
  91   }
  92
  93   public SequenceFeature[] getJalviewSequenceFeatures(
  94           JSONArray jsonSeqFeatures, Sequence seq)
  95   {
  96     SequenceFeature[] seqFeatures = null;
  97     int count = 0;
  98     if (jsonSeqFeatures != null)
  99     {
 100       seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
 101       for (@SuppressWarnings("unchecked")
 102       Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
 103               .hasNext();)
 104       {
 105
 106         SequenceFeature sequenceFeature = new SequenceFeature();
 107         JSONObject jsonFeature = seqFeatureItr.next();
 108         Long begin = (Long) jsonFeature.get("xStart");
 109         Long end = (Long) jsonFeature.get("xEnd");
 110         String type = (String) jsonFeature.get("text");
 111         // String color = (String) jsonFeature.get("fillColor");
 112
 113         sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 114         sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 115         sequenceFeature.setType(type);
 116         seqFeatures[count++] = sequenceFeature;
 117       }
 118     }
 119     return seqFeatures;
 120   }
 121
 122   public void LoadAlignmentFeatures(AlignFrame af)
 123   {
 124
 125     af.setShowSeqFeatures(true);
 126     af.changeColour(cs);
 127     af.setMenusForViewport();
 128   }
 129
 130   private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
 131   {
 132     ColourSchemeI jalviewColor = null;
 133     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
 134             .values())
 135     {
 136       if (cs.getBioJsName().equals(bioJsColourSchemeName))
 137       {
 138         jalviewColor = cs.getJvColourScheme();
 139         break;
 140       }
 141     }
 142     return jalviewColor;
 143   }
 144
 145   @Override
 146   public String print()
 147   {
 148     throw new UnsupportedOperationException(
 149             "Print method of HtmlFile not yet supported!");
 150   }
 151
 152 }