JAL_793 implemented embeding source data in exported html

[jalview.git] / src / jalview / io / HtmlFile.java

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index aadf246..7272830 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -11,9 +11,9 @@ import org.jsoup.nodes.Element;
 
 public class HtmlFile extends AlignFile
 {
-  // public static final String FILE_EXT = "html";
-  //
-  // public static final String FILE_DESC = "HTML";
+  public static final String FILE_EXT = "html";
+
+  public static final String FILE_DESC = "HTML";
 
   private ColourSchemeI cs;
 
@@ -32,7 +32,6 @@ public class HtmlFile extends AlignFile
     super(inFile, type);
   }
 
-  @SuppressWarnings("unchecked")
   @Override
   public void parse() throws IOException
   {
@@ -47,98 +46,25 @@ public class HtmlFile extends AlignFile
 
       Document doc = Jsoup.parse(htmlData.toString());
       Element content = doc.getElementById("seqData");
-
       String alignmentJsonString = content.val();
 
-      new JSONFile().parse(alignmentJsonString);
-
-      // JSONParser jsonParser = new JSONParser();
-      // JSONObject alignmentJsonObj = (JSONObject) jsonParser
-      // .parse(alignmentJsonString);
-      // JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
-      // String bioJsColourScheme = (String) alignmentJsonObj
-      // .get("globalColorScheme");
-      // cs = getJalviewColorScheme(bioJsColourScheme);
-      //
-      // for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator();
-      // sequenceIter
-      // .hasNext();)
-      // {
-      // JSONObject sequence = sequenceIter.next();
-      // String sequcenceString = sequence.get("seq").toString();
-      // Sequence seq = new Sequence(sequence.get("name").toString(),
-      // sequcenceString, Integer.valueOf(sequence.get("start")
-      // .toString()), Integer.valueOf(sequence.get("end")
-      // .toString()));
-      //
-      // JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
-      // SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
-      // jsonSeqArray, seq);
-      // if (retrievedSeqFeatures != null)
-      // {
-      // seq.setSequenceFeatures(retrievedSeqFeatures);
-      // }
-      // seqs.add(seq);
-      //
-      // }
+      JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
+      seqs = jsonFile.seqs;
+      seqGroups = jsonFile.seqGroups;
+      annotations = jsonFile.annotations;
     } catch (Exception e)
     {
       e.printStackTrace();
     }
   }
 
-  // public SequenceFeature[] getJalviewSequenceFeatures(
-  // JSONArray jsonSeqFeatures, Sequence seq)
-  // {
-  // SequenceFeature[] seqFeatures = null;
-  // int count = 0;
-  // if (jsonSeqFeatures != null)
-  // {
-  // seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
-  // for (@SuppressWarnings("unchecked")
-  // Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator();
-  // seqFeatureItr
-  // .hasNext();)
-  // {
-  //
-  // SequenceFeature sequenceFeature = new SequenceFeature();
-  // JSONObject jsonFeature = seqFeatureItr.next();
-  // Long begin = (Long) jsonFeature.get("xStart");
-  // Long end = (Long) jsonFeature.get("xEnd");
-  // String type = (String) jsonFeature.get("text");
-  // // String color = (String) jsonFeature.get("fillColor");
-  //
-  // sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
-  // sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
-  // sequenceFeature.setType(type);
-  // seqFeatures[count++] = sequenceFeature;
-  // }
-  // }
-  // return seqFeatures;
-  // }
-
   public void LoadAlignmentFeatures(AlignFrame af)
   {
-
-    af.setShowSeqFeatures(true);
-    af.changeColour(cs);
+    af.setShowSeqFeatures(JSONFile.isSeqFeaturesEnabled());
+    af.changeColour(JSONFile.getColourScheme());
     af.setMenusForViewport();
   }
 
-  // private ColourSchemeI getJalviewColorScheme(String bioJsColourSchemeName)
-  // {
-  // ColourSchemeI jalviewColor = null;
-  // for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
-  // .values())
-  // {
-  // if (cs.getBioJsName().equals(bioJsColourSchemeName))
-  // {
-  // jalviewColor = cs.getJvColourScheme();
-  // break;
-  // }
-  // }
-  // return jalviewColor;
-  // }
 
   @Override
   public String print()