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 import org.junit.Test;
  15
  16 import com.json.JSONException;
  17
  18 public class BioJsHTMLOutputTest
  19 {
  20
  21
  22   @Test
  23   public void getJalviewAlignmentAsJsonString()
  24   {
  25     BioJsHTMLOutput bioJsHtmlOuput = new BioJsHTMLOutput(null, null);
  26     bioJsHtmlOuput.setGlobalColorScheme("Zappo");
  27
  28     Sequence[] seqs = new Sequence[1];
  29     Sequence seq = new Sequence("name", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1, 26);
  30     // SequenceFeature seqFeature = new SequenceFeature("type", "desc",
  31     // "status", 1, 5, "jalview");
  32     // seq.addSequenceFeature(seqFeature);
  33     seq.setDatasetSequence(seq);
  34     seqs[0] = seq;
  35
  36     Alignment al = new Alignment(seqs);
  37     try
  38     {
  39
  40       JSONParser jsonParser = new JSONParser();
  41       String actualJsonString = bioJsHtmlOuput
  42               .getJalviewAlignmentAsJsonString(al);
  43
  44       JSONObject actualJsonObj = (JSONObject) jsonParser.parse(actualJsonString);
  45
  46       // System.out.println("Output : " + actualJsonString);
  47       Assert.assertTrue(actualJsonObj.get("globalColorScheme") != null);
  48       Assert.assertTrue((actualJsonObj.get("globalColorScheme").toString()).equals("zappo"));
  49
  50       Assert.assertTrue(actualJsonObj.get("webStartUrl") != null);
  51       Assert.assertTrue((actualJsonObj.get("webStartUrl").toString())
  52               .equals("http://www.jalview.org/services/launchApp"));
  53
  54       JSONArray actualSeqJsonObj = (JSONArray) actualJsonObj.get("seqs");
  55       Assert.assertTrue(actualSeqJsonObj != null);
  56       Assert.assertTrue(actualSeqJsonObj.size() == 1);
  57
  58       @SuppressWarnings("unchecked")
  59       Iterator<JSONObject> jsonIter = actualSeqJsonObj.iterator();
  60       JSONObject jsonSeq = jsonIter.next();
  61       Assert.assertTrue(jsonSeq != null);
  62
  63       Assert.assertTrue("'name' cannot be null!",
  64               jsonSeq.get("name") != null);
  65       Assert.assertTrue("Expected name mismatched!",
  66               (jsonSeq.get("name").toString())
  67               .equals("name/1-26"));
  68
  69       Assert.assertTrue("'seq' cannot be null!", jsonSeq.get("seq") != null);
  70       Assert.assertTrue("Expected sequence mismatched!", (jsonSeq
  71               .get("seq").toString())
  72               .equals("ABCDEFGHIJKLMNOPQRSTUVWXYZ"));
  73
  74       Assert.assertTrue("'id' cannot be null!", jsonSeq.get("id") != null);
  75       Assert.assertTrue("Expected id mismatched!",
  76               (jsonSeq.get("id").toString()).equals("1"));
  77
  78       Assert.assertTrue("'start' cannot be null!",
  79               jsonSeq.get("start") != null);
  80       Assert.assertTrue("Expected start mismatched!",
  81               (jsonSeq.get("start").toString()).equals("1"));
  82
  83       Assert.assertTrue("'end' cannot be null!", jsonSeq.get("end") != null);
  84       Assert.assertTrue("Expected end mismatched!",
  85               (jsonSeq.get("end").toString()).equals("26"));
  86
  87       Assert.assertTrue("'features' cannot be null!",
  88               jsonSeq.get("features") != null);
  89       Assert.assertTrue("Expected features mismatched!",
  90               jsonSeq.get("features").toString().equals("[]"));
  91
  92     } catch (IOException e)
  93     {
  94       e.printStackTrace();
  95     } catch (JSONException e)
  96     {
  97       e.printStackTrace();
  98     } catch (ParseException e)
  99     {
 100       e.printStackTrace();
 101     }
 102   }
 103
 104 }