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;
super(inFile, type);
}
- @SuppressWarnings("unchecked")
@Override
public void parse() throws IOException
{
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, 0, sequcenceString.length());
-
- JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
- SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(jsonSeqArray);
- 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)
- {
- SequenceFeature[] seqFeatures = null;
- int count = 0;
- if (jsonSeqFeatures != null)
- {
- seqFeatures = new SequenceFeature[jsonSeqFeatures.size()];
- for (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(begin.intValue());
- sequenceFeature.setEnd(end.intValue());
- 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()