test/jalview/io/BioJsHTMLOutputTest.java

   1 package jalview.io;
   2
   3 import jalview.datamodel.Alignment;
   4 import jalview.datamodel.Sequence;
   5
   6 import java.io.IOException;
   7 import java.util.Iterator;
   8
   9 import org.json.simple.JSONArray;
  10 import org.json.simple.JSONObject;
  11 import org.json.simple.parser.JSONParser;
  12 import org.json.simple.parser.ParseException;
  13 import org.junit.Assert;
  14
  15 import com.json.JSONException;
  16
  17 public class BioJsHTMLOutputTest
  18 {
  19
  20
  21   // @Test
  22   public void getJalviewAlignmentAsJsonString()
  23   {
  24     BioJsHTMLOutput bioJsHtmlOuput = new BioJsHTMLOutput(null, null);
  25     bioJsHtmlOuput.setGlobalColorScheme("Zappo");
  26
  27     Sequence[] seqs = new Sequence[1];
  28     Sequence seq = new Sequence("name", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1, 26);
  29     // SequenceFeature seqFeature = new SequenceFeature("type", "desc",
  30     // "status", 1, 5, "jalview");
  31     // seq.addSequenceFeature(seqFeature);
  32     seq.setDatasetSequence(seq);
  33     seqs[0] = seq;
  34
  35     Alignment al = new Alignment(seqs);
  36     try
  37     {
  38
  39       JSONParser jsonParser = new JSONParser();
  40       String actualJsonString = bioJsHtmlOuput
  41               .getJalviewAlignmentAsJsonString(al);
  42
  43       JSONObject actualJsonObj = (JSONObject) jsonParser.parse(actualJsonString);
  44
  45       // System.out.println("Output : " + actualJsonString);
  46       Assert.assertTrue(actualJsonObj.get("globalColorScheme") != null);
  47       Assert.assertTrue((actualJsonObj.get("globalColorScheme").toString()).equals("zappo"));
  48
  49       Assert.assertTrue(actualJsonObj.get("webStartUrl") != null);
  50       Assert.assertTrue((actualJsonObj.get("webStartUrl").toString())
  51               .equals("http://www.jalview.org/services/launchApp"));
  52
  53       JSONArray actualSeqJsonObj = (JSONArray) actualJsonObj.get("seqs");
  54       Assert.assertTrue(actualSeqJsonObj != null);
  55       Assert.assertTrue(actualSeqJsonObj.size() == 1);
  56
  57       @SuppressWarnings("unchecked")
  58       Iterator<JSONObject> jsonIter = actualSeqJsonObj.iterator();
  59       JSONObject jsonSeq = jsonIter.next();
  60       Assert.assertTrue(jsonSeq != null);
  61
  62       Assert.assertTrue("'name' cannot be null!",
  63               jsonSeq.get("name") != null);
  64       Assert.assertTrue("Expected name mismatched!",
  65               (jsonSeq.get("name").toString())
  66               .equals("name/1-26"));
  67
  68       Assert.assertTrue("'seq' cannot be null!", jsonSeq.get("seq") != null);
  69       Assert.assertTrue("Expected sequence mismatched!", (jsonSeq
  70               .get("seq").toString())
  71               .equals("ABCDEFGHIJKLMNOPQRSTUVWXYZ"));
  72
  73       Assert.assertTrue("'id' cannot be null!", jsonSeq.get("id") != null);
  74       Assert.assertTrue("Expected id mismatched!",
  75               (jsonSeq.get("id").toString()).equals("1"));
  76
  77       Assert.assertTrue("'start' cannot be null!",
  78               jsonSeq.get("start") != null);
  79       Assert.assertTrue("Expected start mismatched!",
  80               (jsonSeq.get("start").toString()).equals("1"));
  81
  82       Assert.assertTrue("'end' cannot be null!", jsonSeq.get("end") != null);
  83       Assert.assertTrue("Expected end mismatched!",
  84               (jsonSeq.get("end").toString()).equals("26"));
  85
  86       Assert.assertTrue("'features' cannot be null!",
  87               jsonSeq.get("features") != null);
  88       Assert.assertTrue("Expected features mismatched!",
  89               jsonSeq.get("features").toString().equals("[]"));
  90
  91     } catch (IOException e)
  92     {
  93       e.printStackTrace();
  94     } catch (JSONException e)
  95     {
  96       e.printStackTrace();
  97     } catch (ParseException e)
  98     {
  99       e.printStackTrace();
 100     }
 101   }
 102
 103 }