src/jalview/io/HtmlFile.java

   1 package jalview.io;
   2
   3 import jalview.gui.AlignFrame;
   4 import jalview.schemes.ColourSchemeI;
   5
   6 import java.io.IOException;
   7
   8 import org.jsoup.Jsoup;
   9 import org.jsoup.nodes.Document;
  10 import org.jsoup.nodes.Element;
  11
  12 public class HtmlFile extends AlignFile
  13 {
  14   // public static final String FILE_EXT = "html";
  15   //
  16   // public static final String FILE_DESC = "HTML";
  17
  18   private ColourSchemeI cs;
  19
  20   public HtmlFile()
  21   {
  22     super();
  23   }
  24
  25   public HtmlFile(FileParse source) throws IOException
  26   {
  27     super(source);
  28   }
  29
  30   public HtmlFile(String inFile, String type) throws IOException
  31   {
  32     super(inFile, type);
  33   }
  34
  35   @SuppressWarnings("unchecked")
  36   @Override
  37   public void parse() throws IOException
  38   {
  39     try
  40     {
  41       StringBuilder htmlData = new StringBuilder();
  42       String currentLine;
  43       while ((currentLine = nextLine()) != null)
  44       {
  45         htmlData.append(currentLine);
  46       }
  47
  48       Document doc = Jsoup.parse(htmlData.toString());
  49       Element content = doc.getElementById("seqData");
  50
  51       String alignmentJsonString = content.val();
  52
  53       new JSONFile().parse(alignmentJsonString);
  54
  55       // JSONParser jsonParser = new JSONParser();
  56       // JSONObject alignmentJsonObj = (JSONObject) jsonParser
  57       // .parse(alignmentJsonString);
  58       // JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
  59       // String bioJsColourScheme = (String) alignmentJsonObj
  60       // .get("globalColorScheme");
  61       // cs = getJalviewColorScheme(bioJsColourScheme);
  62       //
  63       // for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator();
  64       // sequenceIter
  65       // .hasNext();)
  66       // {
  67       // JSONObject sequence = sequenceIter.next();
  68       // String sequcenceString = sequence.get("seq").toString();
  69       // Sequence seq = new Sequence(sequence.get("name").toString(),
  70       // sequcenceString, Integer.valueOf(sequence.get("start")
  71       // .toString()), Integer.valueOf(sequence.get("end")
  72       // .toString()));
  73       //
  74       // JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
  75       // SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
  76       // jsonSeqArray, seq);
  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, Sequence seq)
  92   // {
  93   // SequenceFeature[] seqFeatures = null;
  94   // int count = 0;
  95   // if (jsonSeqFeatures != null)
  96   // {
  97   // seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
  98   // for (@SuppressWarnings("unchecked")
  99   // Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator();
 100   // seqFeatureItr
 101   // .hasNext();)
 102   // {
 103   //
 104   // SequenceFeature sequenceFeature = new SequenceFeature();
 105   // JSONObject jsonFeature = seqFeatureItr.next();
 106   // Long begin = (Long) jsonFeature.get("xStart");
 107   // Long end = (Long) jsonFeature.get("xEnd");
 108   // String type = (String) jsonFeature.get("text");
 109   // // String color = (String) jsonFeature.get("fillColor");
 110   //
 111   // sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
 112   // sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
 113   // sequenceFeature.setType(type);
 114   // seqFeatures[count++] = sequenceFeature;
 115   // }
 116   // }
 117   // return seqFeatures;
 118   // }
 119
 120   public void LoadAlignmentFeatures(AlignFrame af)
 121   {
 122
 123     af.setShowSeqFeatures(true);
 124     af.changeColour(cs);
 125     af.setMenusForViewport();
 126   }
 127
 128   // private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
 129   // {
 130   // ColourSchemeI jalviewColor = null;
 131   // for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
 132   // .values())
 133   // {
 134   // if (cs.getBioJsName().equals(bioJsColourSchemeName))
 135   // {
 136   // jalviewColor = cs.getJvColourScheme();
 137   // break;
 138   // }
 139   // }
 140   // return jalviewColor;
 141   // }
 142
 143   @Override
 144   public String print()
 145   {
 146     throw new UnsupportedOperationException(
 147             "Print method of HtmlFile not yet supported!");
 148   }
 149
 150 }