X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJSONFileTest.java;h=108dd319751f53ee6d4649157ff3a6ac0c7e120b;hb=fddf3084802b37e5cee17829e32692a4aac3e60d;hp=2e28e3a8b9d80fec49cecb2615947d52150a2fd0;hpb=44e5428356c618d139354d02bbfc2f9008ae50b6;p=jalview.git diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java index 2e28e3a..108dd31 100644 --- a/test/jalview/io/JSONFileTest.java +++ b/test/jalview/io/JSONFileTest.java @@ -3,25 +3,30 @@ package jalview.io; import static org.testng.AssertJUnit.assertNotNull; +import jalview.api.AlignExportSettingI; +import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; +import jalview.datamodel.ColumnSelection; 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 jalview.schemes.ZappoColourScheme; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; +import java.util.List; +import org.testng.Assert; import org.testng.AssertJUnit; -import org.testng.annotations.AfterMethod; +import org.testng.annotations.AfterTest; import org.testng.annotations.BeforeMethod; +import org.testng.annotations.BeforeTest; import org.testng.annotations.Test; public class JSONFileTest @@ -33,17 +38,31 @@ public class JSONFileTest private int TEST_ANOT_HEIGHT = 0; - private AlignFrame af; + private int TEST_CS_HEIGHT = 0; - AlignmentI alignment; + private String TEST_JSON_FILE = "examples/example.json"; - AlignmentPanel alignPanel; + private Alignment alignment; - HashMap testSeqs = new HashMap(); - HashMap testAnnots = new HashMap(); - HashMap testGrps = new HashMap(); + private HashMap expectedSeqs = new HashMap(); - @BeforeMethod + private HashMap expectedAnnots = new HashMap(); + + private HashMap expectedGrps = new HashMap(); + + private ColumnSelection expectedColSel = new ColumnSelection(); + + private SequenceI[] expectedHiddenSeqs = new SequenceI[1]; + + private AlignmentI testAlignment; + + private int passedCount; + + private JSONFile testJsonFile; + + private JSONFile jf; + + @BeforeTest public void setup() throws Exception { // create and add sequences @@ -59,6 +78,10 @@ public class JSONFileTest seqs[4] = new Sequence("Q7XA98_TRIPR", "ALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGF", 6, 39); + SequenceI hiddenSeq = new Sequence("FER_TOCH", + "FILGTMISKSFLFRKPAVTSL-KAISNVGE--ALF", 3, 34); + expectedHiddenSeqs[0] = hiddenSeq; + // create and add sequence features SequenceFeature seqFeature2 = new SequenceFeature("feature_x", "desciption", "status", 6, 15, "Jalview"); @@ -70,17 +93,11 @@ public class JSONFileTest 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.setShowSeqFeatures(true); for (Sequence seq : seqs) { seq.setDatasetSequence(seq); - testSeqs.put(seq.getName(), seq); - // jsonFile.seqs.add(seq); + expectedSeqs.put(seq.getName(), seq); } // create and add sequence groups @@ -94,8 +111,8 @@ public class JSONFileTest scheme, true, true, false, 21, 29); seqGrp.setShowNonconserved(false); seqGrp.setDescription(null); - // jsonFile.seqGroups.add(seqGrp); - testGrps.put(seqGrp.getName(), seqGrp); + + expectedGrps.put(seqGrp.getName(), seqGrp); // create and add annotation Annotation[] annot = new Annotation[35]; @@ -137,51 +154,166 @@ public class JSONFileTest AlignmentAnnotation alignAnnot = new AlignmentAnnotation( "Secondary Structure", "New description", annot); - // jsonFile.annotations.add(alignAnnot); - testAnnots.put(alignAnnot.label, alignAnnot); + expectedAnnots.put(alignAnnot.label, alignAnnot); - // Alignment al = new Alignment(seqs); - TEST_SEQ_HEIGHT = testSeqs.size(); - TEST_GRP_HEIGHT = testGrps.size(); - TEST_ANOT_HEIGHT = testAnnots.size(); - } + expectedColSel.hideColumns(32, 33); + expectedColSel.hideColumns(34, 34); - @AfterMethod - public void tearDown() throws Exception - { - } + TEST_SEQ_HEIGHT = expectedSeqs.size(); + TEST_GRP_HEIGHT = expectedGrps.size(); + TEST_ANOT_HEIGHT = expectedAnnots.size(); + TEST_CS_HEIGHT = expectedColSel.getHiddenColumns().size(); - @Test - public void testParse() - { - String jsonFile = "examples/example.json"; - AppletFormatAdapter rf = new AppletFormatAdapter(); - AlignmentI al = null; + AlignExportSettingI exportSettings = new AlignExportSettingI() + { + @Override + public boolean isExportHiddenSequences() + { + return true; + } + + @Override + public boolean isExportHiddenColumns() + { + return true; + } + + @Override + public boolean isExportGroups() + { + return true; + } + + @Override + public boolean isExportFeatures() + { + return true; + } + + @Override + public boolean isExportAnnotations() + { + return true; + } + }; + + AppletFormatAdapter formatAdapter = new AppletFormatAdapter(); try { - al = rf.readFile(jsonFile, AppletFormatAdapter.FILE, - JSONFile.FILE_DESC); + alignment = (Alignment) formatAdapter.readFile(TEST_JSON_FILE, + AppletFormatAdapter.FILE, JSONFile.FILE_DESC); + jf = (JSONFile) formatAdapter.getAlignFile(); + + AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(), + jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures()); + af.changeColour(jf.getColourScheme()); + af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures()); + + + formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings); + String jsonOutput = formatAdapter.formatSequences(JSONFile.FILE_DESC, + af.alignPanel.getAlignment(), false); + + formatAdapter = new AppletFormatAdapter(); + testAlignment = formatAdapter.readFile(jsonOutput, + AppletFormatAdapter.PASTE, JSONFile.FILE_DESC); + testJsonFile = (JSONFile) formatAdapter.getAlignFile(); + // System.out.println(jsonOutput); } catch (IOException e) { e.printStackTrace(); } - assertNotNull("Couldn't read supplied alignment data.", al); - int passedCount = 0; - for (SequenceI seq : al.getSequences()) + } + + @BeforeMethod + public void methodSetup() + { + passedCount = 0; + } + + @AfterTest + public void tearDown() throws Exception + { + testJsonFile = null; + alignment = null; + expectedSeqs = null; + expectedAnnots = null; + expectedGrps = null; + testAlignment = null; + jf = null; + } + + @Test(groups ={ "Functional" }) + public void roundTripTest() + { + assertNotNull("JSON roundtrip test failed!", testJsonFile); + } + + @Test(groups ={ "Functional" }) + public void testSeqParsed() + { + assertNotNull("Couldn't read supplied alignment data.", testAlignment); + Assert.assertNotNull(testAlignment.getSequences()); + for (SequenceI seq : testAlignment.getSequences()) { - SequenceI expectedSeq = testSeqs.get(seq.getName()); - AssertJUnit.assertTrue("Failed Sequence Test for >>> " + seq.getName(), + SequenceI expectedSeq = expectedSeqs.get(seq.getName()); + AssertJUnit.assertTrue( + "Failed Sequence Test for >>> " + seq.getName(), isSeqMatched(expectedSeq, seq)); passedCount++; } AssertJUnit.assertEquals("Some Sequences did not pass the test", TEST_SEQ_HEIGHT, passedCount); + } + + @Test(groups ={ "Functional" }) + public void hiddenColsTest() + { + ColumnSelection cs = testJsonFile.getColumnSelection(); + Assert.assertNotNull(cs); + Assert.assertNotNull(cs.getHiddenColumns()); + List hiddenCols = cs.getHiddenColumns(); + Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT); + Assert.assertEquals(hiddenCols, expectedColSel.getHiddenColumns(), + "Mismatched hidden columns!"); + } - passedCount = 0; - for (SequenceGroup seqGrp : al.getGroups()) + @Test(groups ={ "Functional" }) + public void hiddenSeqsTest() + { + Assert.assertNotNull(testJsonFile.getHiddenSequences(), + "Hidden sequence Expected but found Null"); + Assert.assertEquals(jf.getHiddenSequences().length, 1, + "Hidden sequece"); + } + + @Test(groups ={ "Functional" }) + public void colorSchemeTest() + { + Assert.assertNotNull(testJsonFile.getColourScheme(), + "Colourscheme is null, parsing failed!"); + Assert.assertTrue( + testJsonFile.getColourScheme() instanceof ZappoColourScheme, + "Zappo colour scheme expected!"); + } + + @Test(groups ={ "Functional" }) + public void isShowSeqFeaturesSet() + { + Assert.assertTrue(testJsonFile.isShowSeqFeatures(), + "Sequence feature isDisplayed setting expected to be true"); + } + + @Test(groups ={ "Functional" }) + public void testGrpParsed() + { + Assert.assertNotNull(testAlignment.getGroups()); + for (SequenceGroup seqGrp : testAlignment.getGroups()) { - SequenceGroup expectedGrp = testGrps.get(seqGrp.getName()); + SequenceGroup expectedGrp = expectedGrps.get(seqGrp.getName()); AssertJUnit.assertTrue( "Failed SequenceGroup Test for >>> " + seqGrp.getName(), isGroupMatched(expectedGrp, seqGrp)); @@ -189,21 +321,21 @@ public class JSONFileTest } AssertJUnit.assertEquals("Some SequenceGroups did not pass the test", TEST_GRP_HEIGHT, passedCount); + } - passedCount = 0; - for (AlignmentAnnotation annot : al.getAlignmentAnnotation()) + @Test(groups ={ "Functional" }) + public void testAnnotationParsed() + { + Assert.assertNotNull(testAlignment.getAlignmentAnnotation()); + for (AlignmentAnnotation annot : testAlignment.getAlignmentAnnotation()) { - AlignmentAnnotation expectedAnnot = testAnnots.get(annot.label); + AlignmentAnnotation expectedAnnot = expectedAnnots.get(annot.label); AssertJUnit.assertTrue("Failed AlignmentAnnotation Test for >>> " + annot.label, isAnnotationMatched(expectedAnnot, annot)); passedCount++; } AssertJUnit.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,