X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJSONFileTest.java;fp=test%2Fjalview%2Fio%2FJSONFileTest.java;h=d2960d9035c71e4ddc487d2bb8adf9a2a5a86193;hb=7c5caa07d0f487073d859589149a91ea2b893105;hp=0000000000000000000000000000000000000000;hpb=d62b90cb6effb7b380e5f7d590691dd884b024cf;p=jalview.git

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
new file mode 100644
index 0000000..d2960d9
--- /dev/null
+++ b/test/jalview/io/JSONFileTest.java
@@ -0,0 +1,262 @@
+package jalview.io;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+
+import java.util.ArrayList;
+
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+public class JSONFileTest
+{
+  private JSONFile jsonFile;
+
+  private int TEST_SEQ_HEIGHT = 0;
+
+  private int TEST_GRP_HEIGHT = 0;
+
+  private int TEST_ANOT_HEIGHT = 0;
+
+  @Before
+  public void setUp() throws Exception
+  {
+    jsonFile = new JSONFile();
+
+    // create and add sequences
+    Sequence[] seqs = new Sequence[5];
+    seqs[0] = new Sequence("FER_CAPAN",
+            "SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALF", 3, 34);
+    seqs[1] = new Sequence("FER1_SOLLC",
+            "SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALF", 3, 34);
+    seqs[2] = new Sequence("Q93XJ9_SOLTU",
+            "SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALF", 3, 34);
+    seqs[3] = new Sequence("FER1_PEA",
+            "ALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFL", 6, 37);
+    seqs[4] = new Sequence("Q7XA98_TRIPR",
+            "ALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGF", 6, 39);
+
+    // create and add sequence features
+    SequenceFeature seqFeature2 = new SequenceFeature("feature_x",
+            "desciption", "status", 22, 29, "jalview");
+    SequenceFeature seqFeature3 = new SequenceFeature("feature_x",
+            "desciption", "status", 25, 32, "jalview");
+    SequenceFeature seqFeature4 = new SequenceFeature("feature_x",
+            "desciption", "status", 25, 32, "jalview");
+    seqs[2].addSequenceFeature(seqFeature2);
+    seqs[3].addSequenceFeature(seqFeature3);
+    seqs[4].addSequenceFeature(seqFeature4);
+
+    // add created features to features displayed
+    FeaturesDisplayed fDis = new FeaturesDisplayed();
+    fDis.setVisible("feature_x");
+    jsonFile.setDisplayedFeatures(fDis);
+    JSONFile.setSeqFeaturesEnabled(true);
+
+    for (Sequence seq : seqs)
+    {
+      seq.setDatasetSequence(seq);
+      jsonFile.seqs.add(seq);
+    }
+
+    // create and add sequence groups
+    ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+    grpSeqs.add(seqs[0]);
+    grpSeqs.add(seqs[1]);
+    grpSeqs.add(seqs[2]);
+    ColourSchemeI scheme = jsonFile.getJalviewColorScheme("zappo");
+    SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1114606272",
+            scheme, true, true, false, 2, 9);
+    seqGrp.setShowNonconserved(false);
+    seqGrp.setDescription(null);
+    jsonFile.seqGroups.add(seqGrp);
+
+    // create and add annotation
+    Annotation[] annot = new Annotation[35];
+    annot[0] = new Annotation("", "", '\u0000', 0);
+    annot[1] = new Annotation("", "", '\u0000', 0);
+    annot[2] = new Annotation("α", "", 'H', 0);
+    annot[3] = new Annotation("α", "", 'H', 0);
+    annot[4] = new Annotation("α", "", 'H', 0);
+    annot[5] = new Annotation("α", "", 'H', 0);
+    annot[6] = new Annotation("", "", '\u0000', 0);
+    annot[7] = new Annotation("", "", '\u0000', 0);
+    annot[8] = new Annotation("", "", '\u0000', 0);
+    annot[9] = new Annotation("", "", '\u0000', 0);
+    annot[10] = new Annotation("β", "", 'E', 0);
+    annot[11] = new Annotation("β", "", 'E', 0);
+    annot[12] = new Annotation("", "", '\u0000', 0);
+    annot[13] = new Annotation("", "", '\u0000', 0);
+    annot[14] = new Annotation("", "", '\u0000', 0);
+    annot[15] = new Annotation("", "", '\u0000', 0);
+    annot[16] = new Annotation("α", "", 'H', 0);
+    annot[17] = new Annotation("α", "", 'H', 0);
+    annot[18] = new Annotation("α", "", 'H', 0);
+    annot[19] = new Annotation("α", "", 'H', 0);
+    annot[20] = new Annotation("α", "", 'H', 0);
+
+    annot[21] = new Annotation("", "", '\u0000', 0);
+    annot[22] = new Annotation("", "", '\u0000', 0);
+    annot[23] = new Annotation("", "", '\u0000', 0);
+    annot[24] = new Annotation("", "", '\u0000', 0);
+    annot[25] = new Annotation("", "", '\u0000', 0);
+    annot[26] = new Annotation("", "", '\u0000', 0);
+    annot[27] = new Annotation("", "", '\u0000', 0);
+    annot[28] = new Annotation("", "", '\u0000', 0);
+    annot[29] = new Annotation("", "", '\u0000', 0);
+    annot[30] = new Annotation("", "", '\u0000', 0);
+    annot[31] = new Annotation("", "", '\u0000', 0);
+    annot[32] = new Annotation("β", "", 'E', 0);
+    annot[33] = new Annotation("β", "", 'E', 0);
+    annot[34] = new Annotation("β", "", 'E', 0);
+
+    AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
+            "Secondary Structure", "New description", annot);
+    jsonFile.annotations.add(alignAnnot);
+
+    // Alignment al = new Alignment(seqs);
+    TEST_SEQ_HEIGHT = jsonFile.seqs.size();
+    TEST_GRP_HEIGHT = jsonFile.seqGroups.size();
+    TEST_ANOT_HEIGHT = jsonFile.annotations.size();
+  }
+
+  @After
+  public void tearDown() throws Exception
+  {
+  }
+
+  @Test
+  public void test()
+  {
+    String jsonOuput = jsonFile.print();
+    // System.out.println(">>>>>>>>>>>>>> " + jsonOuput);
+    JSONFile output = new JSONFile().parse(jsonOuput);
+
+    int matchedCounter = 0;
+    for (SequenceI in : jsonFile.getSeqs())
+    {
+      for (SequenceI out : output.getSeqs())
+      {
+        if (in.getName().equals(out.getName())
+                && in.getSequenceAsString().equals(
+                        out.getSequenceAsString())
+                && in.getStart() == out.getStart()
+                && in.getEnd() == out.getEnd() && featuresMatched(in, out))
+        {
+          // System.out.println(">>>> Seq Match Detected");
+          ++matchedCounter;
+        }
+      }
+    }
+    Assert.assertTrue(matchedCounter == TEST_SEQ_HEIGHT);
+
+    matchedCounter = 0;
+    for (SequenceGroup in : jsonFile.getSeqGroups())
+    {
+      for (SequenceGroup out : output.getSeqGroups())
+      {
+        if (in.getName().equals(out.getName())
+                && in.getColourText() == out.getColourText()
+                && in.getDisplayBoxes() == out.getDisplayBoxes()
+                && in.getIgnoreGapsConsensus() == out
+                        .getIgnoreGapsConsensus() && in.cs.equals(out.cs)
+                && in.getSequences().size() == out.getSequences().size())
+        {
+          // System.out.println(">>>> Grp Match Detected");
+          ++matchedCounter;
+        }
+      }
+    }
+    Assert.assertTrue(matchedCounter == TEST_GRP_HEIGHT);
+
+    matchedCounter = 0;
+    for (AlignmentAnnotation in : jsonFile.annotations)
+    {
+      for (AlignmentAnnotation out : output.annotations)
+      {
+        try
+        {
+          // System.out.println("label >>>>> " + in.label + " | " + out.label);
+          // System.out.println("label >>>>> " + in.description + " | "
+          // + out.description);
+          // System.out.println("label >>>>> " + in.annotations.length + " | "
+          // + out.annotations.length);
+          if (in.label.equals(out.label)
+                  && in.description.equals(out.description)
+                && in.annotations.length == out.annotations.length)
+        {
+          ++matchedCounter;
+        }
+        } catch (Exception e)
+        {
+          e.printStackTrace();
+        }
+      }
+    }
+    // System.out.println("matched >>>>> " + matchedCounter + " | "
+    // + TEST_ANOT_HEIGHT);
+    Assert.assertTrue(matchedCounter == TEST_ANOT_HEIGHT);
+
+  }
+
+  private boolean featuresMatched(SequenceI seq1, SequenceI seq2)
+  {
+    boolean matched = false;
+    try
+    {
+      if (seq1 == null && seq2 == null)
+      {
+        return true;
+      }
+
+      SequenceFeature[] inFeature = seq1.getSequenceFeatures();
+      SequenceFeature[] outFeature = seq2.getSequenceFeatures();
+
+      if (inFeature == null && outFeature == null)
+      {
+        return true;
+      }
+      else if ((inFeature == null && outFeature != null)
+              || (inFeature != null && outFeature == null))
+      {
+        return false;
+      }
+
+      int testSize = inFeature.length;
+      int matchedCount = 0;
+      // System.out.println(">>>>>>>>>>>>> 1");
+      for (SequenceFeature in : inFeature)
+      {
+        for (SequenceFeature out : inFeature)
+        {
+          if (inFeature.length == outFeature.length
+                  && in.getBegin() == out.getBegin()
+                  && in.getEnd() == out.getEnd()
+                  && in.getScore() == out.getScore()
+                  && in.getFeatureGroup().equals(out.getFeatureGroup()))
+          {
+
+            ++matchedCount;
+          }
+        }
+      }
+      if (testSize == matchedCount)
+      {
+        matched = true;
+      }
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    // System.out.println(">>>>>>>>>>>>>> features matched : " + matched);
+    return matched;
+  }
+}