package jalview.io;
+
+import static org.junit.Assert.assertNotNull;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
import jalview.schemes.ColourSchemeI;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+import java.io.IOException;
import java.util.ArrayList;
+import java.util.HashMap;
import org.junit.After;
import org.junit.Assert;
public class JSONFileTest
{
- private JSONFile jsonFile;
private int TEST_SEQ_HEIGHT = 0;
private int TEST_ANOT_HEIGHT = 0;
+ private AlignFrame af;
+
+ AlignmentI alignment;
+
+ AlignmentPanel alignPanel;
+
+ HashMap<String, SequenceI> testSeqs = new HashMap<String, SequenceI>();
+ HashMap<String, AlignmentAnnotation> testAnnots = new HashMap<String, AlignmentAnnotation>();
+ HashMap<String, SequenceGroup> testGrps = new HashMap<String, SequenceGroup>();
+
@Before
- public void setUp() throws Exception
+ public void setup() throws Exception
{
- jsonFile = new JSONFile();
-
// create and add sequences
Sequence[] seqs = new Sequence[5];
seqs[0] = new Sequence("FER_CAPAN",
// create and add sequence features
SequenceFeature seqFeature2 = new SequenceFeature("feature_x",
- "desciption", "status", 22, 29, "jalview");
+ "desciption", "status", 6, 15, "Jalview");
SequenceFeature seqFeature3 = new SequenceFeature("feature_x",
- "desciption", "status", 25, 32, "jalview");
+ "desciption", "status", 9, 18, "Jalview");
SequenceFeature seqFeature4 = new SequenceFeature("feature_x",
- "desciption", "status", 25, 32, "jalview");
+ "desciption", "status", 9, 18, "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);
+ // jsonFile.setDisplayedFeatures(fDis);
+ // jsonFile.setShowSeqFeatures(true);
for (Sequence seq : seqs)
{
seq.setDatasetSequence(seq);
- jsonFile.seqs.add(seq);
+ testSeqs.put(seq.getName(), 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);
+ grpSeqs.add(seqs[3]);
+ grpSeqs.add(seqs[4]);
+ ColourSchemeI scheme = JSONFile.getJalviewColorScheme("zappo");
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585",
+ scheme, true, true, false, 21, 29);
seqGrp.setShowNonconserved(false);
seqGrp.setDescription(null);
- jsonFile.seqGroups.add(seqGrp);
+ // jsonFile.seqGroups.add(seqGrp);
+ testGrps.put(seqGrp.getName(), seqGrp);
// create and add annotation
Annotation[] annot = new Annotation[35];
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[5] = new Annotation("", "", '\u0000', 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[8] = new Annotation("β", "", 'E', 0);
+ annot[9] = new Annotation("β", "", 'E', 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[12] = new Annotation("β", "", 'E', 0);
+ annot[13] = new Annotation("β", "", 'E', 0);
+ annot[14] = new Annotation("β", "", 'E', 0);
+ annot[15] = new Annotation("β", "", 'E', 0);
+ annot[16] = new Annotation("", "", '\u0000', 0);
+ annot[17] = new Annotation("", "", '\u0000', 0);
+ annot[18] = new Annotation("", "", '\u0000', 0);
+ annot[19] = new Annotation("", "", '\u0000', 0);
+ annot[20] = new Annotation("", "", '\u0000', 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[26] = new Annotation("α", "", 'H', 0);
+ annot[27] = new Annotation("α", "", 'H', 0);
+ annot[28] = new Annotation("α", "", 'H', 0);
+ annot[29] = new Annotation("α", "", 'H', 0);
+ annot[30] = new Annotation("α", "", 'H', 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);
+ annot[32] = new Annotation("", "", '\u0000', 0);
+ annot[33] = new Annotation("", "", '\u0000', 0);
+ annot[34] = new Annotation("", "", '\u0000', 0);
AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
"Secondary Structure", "New description", annot);
- jsonFile.annotations.add(alignAnnot);
+ // jsonFile.annotations.add(alignAnnot);
+ testAnnots.put(alignAnnot.label, alignAnnot);
// Alignment al = new Alignment(seqs);
- TEST_SEQ_HEIGHT = jsonFile.seqs.size();
- TEST_GRP_HEIGHT = jsonFile.seqGroups.size();
- TEST_ANOT_HEIGHT = jsonFile.annotations.size();
+ TEST_SEQ_HEIGHT = testSeqs.size();
+ TEST_GRP_HEIGHT = testGrps.size();
+ TEST_ANOT_HEIGHT = testAnnots.size();
}
@After
}
@Test
- public void test()
+ public void testParse()
{
- String jsonOuput = jsonFile.print();
- // System.out.println(">>>>>>>>>>>>>> " + jsonOuput);
- JSONFile output = new JSONFile().parse(jsonOuput);
+ String jsonFile = "examples/example.json";
+ AppletFormatAdapter rf = new AppletFormatAdapter();
+ AlignmentI al = null;
+ try
+ {
+ al = rf.readFile(jsonFile, AppletFormatAdapter.FILE,
+ JSONFile.FILE_DESC);
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ assertNotNull("Couldn't read supplied alignment data.", al);
- int matchedCounter = 0;
- for (SequenceI in : jsonFile.getSeqs())
+ int passedCount = 0;
+ for (SequenceI seq : al.getSequences())
{
- 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;
- }
- }
+ SequenceI expectedSeq = testSeqs.get(seq.getName());
+ Assert.assertTrue("Failed Sequence Test for >>> " + seq.getName(),
+ isSeqMatched(expectedSeq, seq));
+ passedCount++;
}
- Assert.assertTrue(matchedCounter == TEST_SEQ_HEIGHT);
+ Assert.assertEquals("Some Sequences did not pass the test",
+ TEST_SEQ_HEIGHT, passedCount);
- matchedCounter = 0;
- for (SequenceGroup in : jsonFile.getSeqGroups())
+ passedCount = 0;
+ for (SequenceGroup seqGrp : al.getGroups())
{
- 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;
- }
- }
+ SequenceGroup expectedGrp = testGrps.get(seqGrp.getName());
+ Assert.assertTrue(
+ "Failed SequenceGroup Test for >>> " + seqGrp.getName(),
+ isGroupMatched(expectedGrp, seqGrp));
+ passedCount++;
}
- Assert.assertTrue(matchedCounter == TEST_GRP_HEIGHT);
+ Assert.assertEquals("Some SequenceGroups did not pass the test",
+ TEST_GRP_HEIGHT, passedCount);
- matchedCounter = 0;
- for (AlignmentAnnotation in : jsonFile.annotations)
+ passedCount = 0;
+ for (AlignmentAnnotation annot : al.getAlignmentAnnotation())
{
- for (AlignmentAnnotation out : output.annotations)
+ AlignmentAnnotation expectedAnnot = testAnnots.get(annot.label);
+ Assert.assertTrue("Failed AlignmentAnnotation Test for >>> "
+ + annot.label, isAnnotationMatched(expectedAnnot, annot));
+ passedCount++;
+ }
+ Assert.assertEquals("Some Sequences did not pass the test",
+ TEST_ANOT_HEIGHT, passedCount);
+
+ // af = new AlignFrame(al, 700, 500);
+ // AlignViewport viewport = af.getViewport();
+ // alignPanel = new AlignmentPanel(af, viewport);
+ }
+
+ public boolean isAnnotationMatched(AlignmentAnnotation eAnnot,
+ AlignmentAnnotation annot)
+ {
+ if (!eAnnot.label.equals(annot.label)
+ || !eAnnot.description.equals(annot.description)
+ || eAnnot.annotations.length != annot.annotations.length)
+ {
+ return false;
+ }
+
+ for (int x = 0; x < annot.annotations.length; x++)
+ {
+ Annotation y = annot.annotations[x];
+ Annotation z = annot.annotations[x];
+
+ if (!y.displayCharacter.equals(z.displayCharacter)
+ || y.value != z.value
+ || y.secondaryStructure != z.secondaryStructure)
{
- 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();
- }
+ return false;
}
}
- // System.out.println("matched >>>>> " + matchedCounter + " | "
- // + TEST_ANOT_HEIGHT);
- Assert.assertTrue(matchedCounter == TEST_ANOT_HEIGHT);
+ return true;
+ }
+
+ public boolean isSeqMatched(SequenceI expectedSeq, SequenceI actualSeq)
+ {
+ System.out.println("Testing >>> " + actualSeq.getName());
+
+ if (expectedSeq.getName().equals(actualSeq.getName())
+ && expectedSeq.getSequenceAsString().equals(
+ actualSeq.getSequenceAsString())
+ && expectedSeq.getStart() == actualSeq.getStart()
+ && expectedSeq.getEnd() == actualSeq.getEnd()
+ && featuresMatched(expectedSeq, actualSeq))
+ {
+ return true;
+ }
+ return false;
+ }
+ public boolean isGroupMatched(SequenceGroup expectedGrp,
+ SequenceGroup actualGrp)
+ {
+
+ System.out.println("Testing >>> " + actualGrp.getName());
+ System.out.println(expectedGrp.getName() + " | " + actualGrp.getName());
+ System.out.println(expectedGrp.getColourText() + " | "
+ + actualGrp.getColourText());
+ System.out.println(expectedGrp.getDisplayBoxes() + " | "
+ + actualGrp.getDisplayBoxes());
+ System.out.println(expectedGrp.getIgnoreGapsConsensus() + " | "
+ + actualGrp.getIgnoreGapsConsensus());
+ System.out.println(expectedGrp.getSequences().size() + " | "
+ + actualGrp.getSequences().size());
+ System.out.println(expectedGrp.getStartRes() + " | "
+ + actualGrp.getStartRes());
+ System.out.println(expectedGrp.getEndRes() + " | "
+ + actualGrp.getEndRes());
+
+ if (expectedGrp.getName().equals(actualGrp.getName())
+ && expectedGrp.getColourText() == actualGrp.getColourText()
+ && expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
+ && expectedGrp.getIgnoreGapsConsensus() == actualGrp
+ .getIgnoreGapsConsensus()
+ && expectedGrp.cs.equals(actualGrp.cs)
+ && expectedGrp.getSequences().size() == actualGrp
+ .getSequences().size()
+ && expectedGrp.getStartRes() == actualGrp.getStartRes()
+ && expectedGrp.getEndRes() == actualGrp.getEndRes())
+ {
+ return true;
+ }
+ return false;
}
private boolean featuresMatched(SequenceI seq1, SequenceI seq2)
int testSize = inFeature.length;
int matchedCount = 0;
- // System.out.println(">>>>>>>>>>>>> 1");
for (SequenceFeature in : inFeature)
{
- for (SequenceFeature out : inFeature)
+ for (SequenceFeature out : outFeature)
{
+ System.out.println(out.getType() + " | " + in.getType());
+ System.out.println(out.getBegin() + " | " + in.getBegin());
+ System.out.println(out.getEnd() + " | " + in.getEnd());
+
if (inFeature.length == outFeature.length
&& in.getBegin() == out.getBegin()
&& in.getEnd() == out.getEnd()
&& in.getScore() == out.getScore()
- && in.getFeatureGroup().equals(out.getFeatureGroup()))
+ && in.getFeatureGroup().equals(out.getFeatureGroup())
+ && in.getType().equals(out.getType()))
{
++matchedCount;
}
}
}
+ System.out.println("matched count >>>>>> " + matchedCount);
if (testSize == matchedCount)
{
matched = true;
git://source.jalview.org / jalview.git / blobdiff