import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueColourScheme;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import org.testng.Assert;
import org.testng.AssertJUnit;
private Alignment alignment;
- private HashMap<String, SequenceI> expectedSeqs = new HashMap<String, SequenceI>();
+ private HashMap<String, SequenceI> expectedSeqs = new HashMap<>();
- private HashMap<String, AlignmentAnnotation> expectedAnnots = new HashMap<String, AlignmentAnnotation>();
+ private HashMap<String, AlignmentAnnotation> expectedAnnots = new HashMap<>();
- private HashMap<String, SequenceGroup> expectedGrps = new HashMap<String, SequenceGroup>();
+ private HashMap<String, SequenceGroup> expectedGrps = new HashMap<>();
- private ColumnSelection expectedColSel = new ColumnSelection();
+ private HiddenColumns expectedColSel = new HiddenColumns();
private SequenceI[] expectedHiddenSeqs = new SequenceI[1];
private JSONFile jf;
+ private AlignExportSettingI exportSettings;
+
@BeforeTest(alwaysRun = true)
public void setup() throws Exception
{
+ /*
+ * construct expected values
+ * nb this have to match the data in examples/example.json
+ */
// 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", 6, 15, "Jalview");
+ "theDesc", 6, 15, "Jalview");
SequenceFeature seqFeature3 = new SequenceFeature("feature_x",
- "desciption", "status", 9, 18, "Jalview");
+ "theDesc", 9, 18, "Jalview");
SequenceFeature seqFeature4 = new SequenceFeature("feature_x",
- "desciption", "status", 9, 18, "Jalview");
+ "theDesc", 9, 18, "Jalview");
+ // non-positional feature:
+ SequenceFeature seqFeature5 = new SequenceFeature("Domain",
+ "My description", 0, 0, "Pfam");
seqs[2].addSequenceFeature(seqFeature2);
seqs[3].addSequenceFeature(seqFeature3);
seqs[4].addSequenceFeature(seqFeature4);
+ seqs[2].addSequenceFeature(seqFeature5);
for (Sequence seq : seqs)
{
expectedSeqs.put(seq.getName(), seq);
}
- // create and add sequence groups
- ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+ // create and add a sequence group
+ List<SequenceI> grpSeqs = new ArrayList<>();
grpSeqs.add(seqs[1]);
grpSeqs.add(seqs[2]);
grpSeqs.add(seqs[3]);
grpSeqs.add(seqs[4]);
- SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585",
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs,
+ "JGroup:1883305585",
null, true, true, false, 21, 29);
ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
"zappo", seqGrp);
- seqGrp.cs = scheme;
+ seqGrp.cs.setColourScheme(scheme);
seqGrp.setShowNonconserved(false);
seqGrp.setDescription(null);
TEST_SEQ_HEIGHT = expectedSeqs.size();
TEST_GRP_HEIGHT = expectedGrps.size();
TEST_ANOT_HEIGHT = expectedAnnots.size();
- TEST_CS_HEIGHT = expectedColSel.getHiddenColumns().size();
+ TEST_CS_HEIGHT = expectedColSel.getHiddenColumnsCopy().size();
- AlignExportSettingI exportSettings = new AlignExportSettingI()
+ exportSettings = new AlignExportSettingI()
{
@Override
public boolean isExportHiddenSequences()
jf = (JSONFile) formatAdapter.getAlignFile();
AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(),
- jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
+ jf.getHiddenColumns(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
String colourSchemeName = jf.getGlobalColourScheme();
@Test(groups = { "Functional" })
public void hiddenColsTest()
{
- ColumnSelection cs = testJsonFile.getColumnSelection();
+ HiddenColumns cs = testJsonFile.getHiddenColumns();
Assert.assertNotNull(cs);
- Assert.assertNotNull(cs.getHiddenColumns());
- List<int[]> hiddenCols = cs.getHiddenColumns();
+ Assert.assertNotNull(cs.getHiddenColumnsCopy());
+ List<int[]> hiddenCols = cs.getHiddenColumnsCopy();
Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
Assert.assertEquals(hiddenCols.get(0), expectedColSel
- .getHiddenColumns().get(0),
+ .getHiddenColumnsCopy().get(0),
"Mismatched hidden columns!");
}
"Zappo colour scheme expected!");
}
+ /**
+ * Test for bug JAL-2489, NPE when exporting BioJSON with global colour
+ * scheme, and a group colour scheme, set as 'None'
+ */
+ @Test(groups = { "Functional" })
+ public void testBioJSONRoundTripWithColourSchemeNone()
+ {
+ AppletFormatAdapter formatAdapter = new AppletFormatAdapter();
+
+ Alignment _alignment;
+ try
+ {
+ // load example BioJSON file
+ _alignment = (Alignment) formatAdapter.readFile(TEST_JSON_FILE,
+ DataSourceType.FILE, FileFormat.Json);
+ JSONFile bioJsonFile = (JSONFile) formatAdapter.getAlignFile();
+ AlignFrame alignFrame = new AlignFrame(_alignment,
+ bioJsonFile.getHiddenSequences(),
+ bioJsonFile.getHiddenColumns(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ /*
+ * Create a group on the alignment;
+ * Change global and group colour scheme to 'None' and perform round trip
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(_alignment.getSequenceAt(0), false);
+ sg.setColourScheme(null);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ ResidueColourScheme.NONE, _alignment);
+ alignFrame.changeColour(cs);
+ alignFrame.getViewport().setFeaturesDisplayed(
+ bioJsonFile.getDisplayedFeatures());
+ formatAdapter = new AppletFormatAdapter(alignFrame.alignPanel,
+ exportSettings);
+ // export BioJSON string
+ String jsonOutput = formatAdapter.formatSequences(FileFormat.Json,
+ alignFrame.alignPanel.getAlignment(), false);
+ // read back Alignment from BioJSON string
+ formatAdapter = new AppletFormatAdapter();
+ formatAdapter.readFile(jsonOutput, DataSourceType.PASTE,
+ FileFormat.Json);
+ // assert 'None' colour scheme is retained after round trip
+ JSONFile _bioJsonFile = (JSONFile) formatAdapter.getAlignFile();
+ Assert.assertEquals(_bioJsonFile.getGlobalColourScheme(),
+ ResidueColourScheme.NONE);
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+
@Test(groups = { "Functional" })
public void isShowSeqFeaturesSet()
{
return true;
}
- public boolean isSeqMatched(SequenceI expectedSeq, SequenceI actualSeq)
+ boolean isSeqMatched(SequenceI expectedSeq, SequenceI actualSeq)
{
System.out.println("Testing >>> " + actualSeq.getName());
+ actualGrp.getStartRes());
System.out.println(expectedGrp.getEndRes() + " | "
+ actualGrp.getEndRes());
- System.out.println(expectedGrp.cs + " | " + actualGrp.cs);
+ System.out.println(expectedGrp.cs.getColourScheme() + " | "
+ + actualGrp.cs.getColourScheme());
+ boolean colourSchemeMatches = (expectedGrp.cs.getColourScheme() == null && actualGrp.cs
+ .getColourScheme() == null)
+ || expectedGrp.cs.getColourScheme().getClass()
+ .equals(actualGrp.cs.getColourScheme().getClass());
if (expectedGrp.getName().equals(actualGrp.getName())
&& expectedGrp.getColourText() == actualGrp.getColourText()
&& expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
&& expectedGrp.getIgnoreGapsConsensus() == actualGrp
.getIgnoreGapsConsensus()
- && (expectedGrp.cs.getClass().equals(actualGrp.cs.getClass()))
+ && colourSchemeMatches
&& expectedGrp.getSequences().size() == actualGrp
.getSequences().size()
&& expectedGrp.getStartRes() == actualGrp.getStartRes()
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();
+ List<SequenceFeature> inFeature = seq1.getFeatures().getAllFeatures();
+ List<SequenceFeature> outFeature = seq2.getFeatures()
+ .getAllFeatures();
- if (inFeature == null && outFeature == null)
- {
- return true;
- }
- else if ((inFeature == null && outFeature != null)
- || (inFeature != null && outFeature == null))
+ if (inFeature.size() != outFeature.size())
{
+ System.err.println("Feature count in: " + inFeature.size()
+ + ", out: " + outFeature.size());
return false;
}
- int testSize = inFeature.length;
- int matchedCount = 0;
+ SequenceFeatures.sortFeatures(inFeature, true);
+ SequenceFeatures.sortFeatures(outFeature, true);
+ int i = 0;
for (SequenceFeature in : inFeature)
{
- for (SequenceFeature out : outFeature)
+ SequenceFeature out = outFeature.get(i);
+ /*
+ System.out.println(out.getType() + " | " + in.getType());
+ System.out.println(out.getBegin() + " | " + in.getBegin());
+ System.out.println(out.getEnd() + " | " + in.getEnd());
+ */
+ if (!in.equals(out))
{
- 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.getType().equals(out.getType()))
- {
-
- ++matchedCount;
- }
+ System.err.println("Mismatch of " + in.toString() + " "
+ + out.toString());
+ return false;
}
- }
- System.out.println("matched count >>>>>> " + matchedCount);
- if (testSize == matchedCount)
- {
- matched = true;
+ /*
+ if (in.getBegin() == out.getBegin() && in.getEnd() == out.getEnd()
+ && in.getScore() == out.getScore()
+ && in.getFeatureGroup().equals(out.getFeatureGroup())
+ && in.getType().equals(out.getType())
+ && mapsMatch(in.otherDetails, out.otherDetails))
+ {
+ }
+ else
+ {
+ System.err.println("Feature[" + i + "] mismatch, in: "
+ + in.toString() + ", out: "
+ + outFeature.get(i).toString());
+ return false;
+ }
+ */
+ i++;
}
} catch (Exception e)
{
e.printStackTrace();
}
// System.out.println(">>>>>>>>>>>>>> features matched : " + matched);
- return matched;
+ return true;
+ }
+
+ boolean mapsMatch(Map<String, Object> m1, Map<String, Object> m2)
+ {
+ if (m1 == null || m2 == null)
+ {
+ if (m1 != null || m2 != null)
+ {
+ System.err
+ .println("only one SequenceFeature.otherDetails is not null");
+ return false;
+ }
+ else
+ {
+ return true;
+ }
+ }
+ if (m1.size() != m2.size())
+ {
+ System.err.println("otherDetails map different sizes");
+ return false;
+ }
+ for (String key : m1.keySet())
+ {
+ if (!m2.containsKey(key))
+ {
+ System.err.println(key + " in only one otherDetails");
+ return false;
+ }
+ if (m1.get(key) == null && m2.get(key) != null || m1.get(key) != null
+ && m2.get(key) == null || !m1.get(key).equals(m2.get(key)))
+ {
+ System.err.println(key + " values in otherDetails don't match");
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Test group roundtrip with null (None) group colour scheme
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testGrpParsed_colourNone() throws IOException
+ {
+ AlignmentI copy = new Alignment(testAlignment);
+ SequenceGroup sg = testAlignment.getGroups().get(0);
+ SequenceGroup copySg = new SequenceGroup(new ArrayList<SequenceI>(),
+ sg.getName(),
+ null, sg.getDisplayBoxes(), sg.getDisplayText(),
+ sg.getColourText(), sg.getStartRes(), sg.getEndRes());
+ for (SequenceI seq : sg.getSequences())
+ {
+ int seqIndex = testAlignment.findIndex(seq);
+ copySg.addSequence(copy.getSequenceAt(seqIndex), false);
+ }
+ copy.addGroup(copySg);
+
+ AlignFrame af = new AlignFrame(copy, copy.getWidth(), copy.getHeight());
+ AppletFormatAdapter formatAdapter = new AppletFormatAdapter(
+ af.alignPanel);
+ String jsonOutput = formatAdapter.formatSequences(FileFormat.Json,
+ copy, false);
+ formatAdapter = new AppletFormatAdapter();
+ AlignmentI newAlignment = formatAdapter.readFile(jsonOutput,
+ DataSourceType.PASTE, FileFormat.Json);
+
+ Assert.assertNotNull(newAlignment.getGroups());
+ for (SequenceGroup seqGrp : newAlignment.getGroups())
+ {
+ SequenceGroup expectedGrp = copySg;
+ AssertJUnit.assertTrue(
+ "Failed SequenceGroup Test for >>> " + seqGrp.getName(),
+ isGroupMatched(expectedGrp, seqGrp));
+ passedCount++;
+ }
+ AssertJUnit.assertEquals("Some SequenceGroups did not pass the test",
+ TEST_GRP_HEIGHT, passedCount);
}
}
git://source.jalview.org / jalview.git / blobdiff