package jalview.io;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.Sequence;
+import org.junit.Ignore;
+import org.junit.Test;
-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.json.simple.parser.ParseException;
-import org.junit.Assert;
-
-import com.json.JSONException;
public class BioJsHTMLOutputTest
{
- // @Test
+ @Test
+ @Ignore
public void getJalviewAlignmentAsJsonString()
{
BioJsHTMLOutput bioJsHtmlOuput = new BioJsHTMLOutput(null, null);
- bioJsHtmlOuput.setGlobalColorScheme("Zappo");
-
- Sequence[] seqs = new Sequence[1];
- Sequence seq = new Sequence("name", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1, 26);
- // SequenceFeature seqFeature = new SequenceFeature("type", "desc",
- // "status", 1, 5, "jalview");
- // seq.addSequenceFeature(seqFeature);
- seq.setDatasetSequence(seq);
- seqs[0] = seq;
-
- Alignment al = new Alignment(seqs);
- try
- {
-
- JSONParser jsonParser = new JSONParser();
- String actualJsonString = bioJsHtmlOuput
- .getJalviewAlignmentAsJsonString(al);
-
- JSONObject actualJsonObj = (JSONObject) jsonParser.parse(actualJsonString);
-
- // System.out.println("Output : " + actualJsonString);
- Assert.assertTrue(actualJsonObj.get("globalColorScheme") != null);
- Assert.assertTrue((actualJsonObj.get("globalColorScheme").toString()).equals("zappo"));
-
- Assert.assertTrue(actualJsonObj.get("webStartUrl") != null);
- Assert.assertTrue((actualJsonObj.get("webStartUrl").toString())
- .equals("http://www.jalview.org/services/launchApp"));
-
- JSONArray actualSeqJsonObj = (JSONArray) actualJsonObj.get("seqs");
- Assert.assertTrue(actualSeqJsonObj != null);
- Assert.assertTrue(actualSeqJsonObj.size() == 1);
-
- @SuppressWarnings("unchecked")
- Iterator<JSONObject> jsonIter = actualSeqJsonObj.iterator();
- JSONObject jsonSeq = jsonIter.next();
- Assert.assertTrue(jsonSeq != null);
-
- Assert.assertTrue("'name' cannot be null!",
- jsonSeq.get("name") != null);
- Assert.assertTrue("Expected name mismatched!",
- (jsonSeq.get("name").toString())
- .equals("name/1-26"));
-
- Assert.assertTrue("'seq' cannot be null!", jsonSeq.get("seq") != null);
- Assert.assertTrue("Expected sequence mismatched!", (jsonSeq
- .get("seq").toString())
- .equals("ABCDEFGHIJKLMNOPQRSTUVWXYZ"));
-
- Assert.assertTrue("'id' cannot be null!", jsonSeq.get("id") != null);
- Assert.assertTrue("Expected id mismatched!",
- (jsonSeq.get("id").toString()).equals("1"));
-
- Assert.assertTrue("'start' cannot be null!",
- jsonSeq.get("start") != null);
- Assert.assertTrue("Expected start mismatched!",
- (jsonSeq.get("start").toString()).equals("1"));
-
- Assert.assertTrue("'end' cannot be null!", jsonSeq.get("end") != null);
- Assert.assertTrue("Expected end mismatched!",
- (jsonSeq.get("end").toString()).equals("26"));
-
- Assert.assertTrue("'features' cannot be null!",
- jsonSeq.get("features") != null);
- Assert.assertTrue("Expected features mismatched!",
- jsonSeq.get("features").toString().equals("[]"));
- } catch (IOException e)
- {
- e.printStackTrace();
- } catch (JSONException e)
- {
- e.printStackTrace();
- } catch (ParseException e)
- {
- e.printStackTrace();
- }
}
}