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.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 HtmlFile() {
- super();
- }
-
- public HtmlFile(FileParse source) throws IOException {
- super(source);
- }
-
- public HtmlFile(String inFile, String type) throws IOException {
- super(inFile, type);
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public void parse() throws IOException {
- try {
- StringBuilder htmlData = new StringBuilder();
- String currentLine;
- while ((currentLine = nextLine()) != null) {
- htmlData.append(currentLine);
- }
-
- Document doc = Jsoup.parse(htmlData.toString());
- Element content = doc.getElementById("seqData");
-
- String alignmentJsonString = "{\"seqs\":" + content.val() + "}";
- JSONParser jsonParser = new JSONParser();
- JSONObject alignmentJsonObj = (JSONObject) jsonParser.parse(alignmentJsonString);
- JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
-
- for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter.hasNext();) {
- JSONObject sequence = sequenceIter.next();
- System.out.println(sequence.get("id").toString() + " " + sequence.get("name"));
- String sequcenceString = sequence.get("seq").toString();
- Sequence seq = new Sequence(sequence.get("name").toString(), sequcenceString, 0, sequcenceString.length());
- seqs.add(seq);
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- @Override
- public String print() {
- throw new UnsupportedOperationException("Print method of HtmlFile not yet supported!");
- }
+public class HtmlFile extends AlignFile
+{
+ public static final String FILE_EXT = "html";
+
+ public static final String FILE_DESC = "HTML";
+
+ private ColourSchemeI cs;
+
+ public HtmlFile()
+ {
+ super();
+ }
+
+ public HtmlFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ public HtmlFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public void parse() throws IOException
+ {
+ try
+ {
+ StringBuilder htmlData = new StringBuilder();
+ String currentLine;
+ while ((currentLine = nextLine()) != null)
+ {
+ htmlData.append(currentLine);
+ }
+
+ 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);
+
+ }
+ } 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.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()
+ {
+ throw new UnsupportedOperationException(
+ "Print method of HtmlFile not yet supported!");
+ }
}