X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=72728300b8b1c627631ca6a383cb4b29a2d9e71f;hb=5d59bb58f5bcecc6b240d125e13bbe1f1868f681;hp=3cb7c3fc612c7af895aa948d02e0c7d7780c8587;hpb=36c3d72e0344f1aaa2137dca8eba829e7395f05a;p=jalview.git

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 3cb7c3f..7272830 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,26 +1,19 @@
 package jalview.io;
 
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
 import jalview.gui.AlignFrame;
-import jalview.json.binding.v1.BioJsAlignmentPojo.JalviewBioJsColorSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 
 import java.io.IOException;
-import java.util.Iterator;
 
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
 import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
 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;
 
@@ -39,7 +32,6 @@ public class HtmlFile extends AlignFile
     super(inFile, type);
   }
 
-  @SuppressWarnings("unchecked")
   @Override
   public void parse() throws IOException
   {
@@ -54,93 +46,25 @@ public class HtmlFile extends AlignFile
 
       Document doc = Jsoup.parse(htmlData.toString());
       Element content = doc.getElementById("seqData");
-
       String alignmentJsonString = content.val();
-      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()