X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJSONFileTest.java;h=acde68d35e5af65a85c72d51d239bfc94f005148;hb=4bb1a8a4b8fc08ed5b0d51f0ea03d9a9ad7dc419;hp=bce9795860519120f0e1d5f22a16b393e9866664;hpb=6dd554fdbf34db6b79595d5027159d20225f4894;p=jalview.git
diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index bce9795..acde68d 100644
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -1,48 +1,99 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
+import static org.testng.AssertJUnit.assertNotNull;
-import static org.junit.Assert.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.gui.JvOptionPane;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
-import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+import jalview.schemes.ResidueColourScheme;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
-import org.junit.After;
-import org.junit.Assert;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterTest;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
public class JSONFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private int TEST_SEQ_HEIGHT = 0;
private int TEST_GRP_HEIGHT = 0;
private int TEST_ANOT_HEIGHT = 0;
- private AlignFrame af;
+ private int TEST_CS_HEIGHT = 0;
+
+ private String TEST_JSON_FILE = "examples/example.json";
+
+ private Alignment alignment;
+
+ private HashMap expectedSeqs = new HashMap();
+
+ private HashMap expectedAnnots = new HashMap();
- AlignmentI alignment;
+ private HashMap expectedGrps = new HashMap();
- AlignmentPanel alignPanel;
+ private ColumnSelection expectedColSel = new ColumnSelection();
- HashMap testSeqs = new HashMap();
- HashMap testAnnots = new HashMap();
- HashMap testGrps = new HashMap();
+ private SequenceI[] expectedHiddenSeqs = new SequenceI[1];
- @Before
+ private AlignmentI testAlignment;
+
+ private int passedCount;
+
+ private JSONFile testJsonFile;
+
+ private JSONFile jf;
+
+ private AlignExportSettingI exportSettings;
+
+ @BeforeTest(alwaysRun = true)
public void setup() throws Exception
{
// create and add sequences
@@ -58,6 +109,10 @@ 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");
@@ -69,32 +124,28 @@ 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);
+ seq.createDatasetSequence();
+ expectedSeqs.put(seq.getName(), seq);
}
- // create and add sequence groups
- ArrayList grpSeqs = new ArrayList();
+ // create and add a sequence group
+ List grpSeqs = new ArrayList();
grpSeqs.add(seqs[1]);
grpSeqs.add(seqs[2]);
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);
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs,
+ "JGroup:1883305585",
+ null, true, true, false, 21, 29);
+ ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
+ "zappo", seqGrp);
+ seqGrp.cs.setColourScheme(scheme);
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];
@@ -136,73 +187,248 @@ 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);
- @After
- 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;
+ 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;
+ }
+
+ @Override
+ public boolean isCancelled()
+ {
+ return false;
+ }
+ };
+
+ AppletFormatAdapter formatAdapter = new AppletFormatAdapter();
try
{
- al = rf.readFile(jsonFile, AppletFormatAdapter.FILE,
- JSONFile.FILE_DESC);
+ alignment = (Alignment) formatAdapter.readFile(TEST_JSON_FILE,
+ DataSourceType.FILE, FileFormat.Json);
+ jf = (JSONFile) formatAdapter.getAlignFile();
+
+ AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(),
+ jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
+ String colourSchemeName = jf.getGlobalColourScheme();
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, alignment);
+ af.changeColour(cs);
+ af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
+
+ formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
+ String jsonOutput = formatAdapter.formatSequences(FileFormat.Json,
+ af.alignPanel.getAlignment(), false);
+
+ formatAdapter = new AppletFormatAdapter();
+ testAlignment = formatAdapter.readFile(jsonOutput,
+ DataSourceType.PASTE, FileFormat.Json);
+ 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(alwaysRun = true)
+ public void methodSetup()
+ {
+ passedCount = 0;
+ }
+
+ @AfterTest(alwaysRun = true)
+ 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());
- Assert.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++;
}
- Assert.assertEquals("Some Sequences did not pass the test",
+ AssertJUnit.assertEquals("Some Sequences did not pass the test",
TEST_SEQ_HEIGHT, passedCount);
+ }
- passedCount = 0;
- for (SequenceGroup seqGrp : al.getGroups())
+ @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.get(0), expectedColSel
+ .getHiddenColumns().get(0),
+ "Mismatched hidden columns!");
+ }
+
+ @Test(groups = { "Functional" })
+ public void hiddenSeqsTest()
+ {
+ Assert.assertNotNull(testJsonFile.getHiddenSequences(),
+ "Hidden sequence Expected but found Null");
+ Assert.assertEquals(jf.getHiddenSequences().length, 1,
+ "Hidden sequence");
+ }
+
+ @Test(groups = { "Functional" })
+ public void colorSchemeTest()
+ {
+ Assert.assertNotNull(testJsonFile.getGlobalColourScheme(),
+ "Colourscheme is null, parsing failed!");
+ Assert.assertEquals(testJsonFile.getGlobalColourScheme(), "Zappo",
+ "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.getColumnSelection(), 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)
{
- SequenceGroup expectedGrp = testGrps.get(seqGrp.getName());
- Assert.assertTrue(
+ e.printStackTrace();
+ }
+ }
+
+ @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 = expectedGrps.get(seqGrp.getName());
+ AssertJUnit.assertTrue(
"Failed SequenceGroup Test for >>> " + seqGrp.getName(),
isGroupMatched(expectedGrp, seqGrp));
passedCount++;
}
- Assert.assertEquals("Some SequenceGroups did not pass the test",
+ 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);
- Assert.assertTrue("Failed AlignmentAnnotation Test for >>> "
+ AlignmentAnnotation expectedAnnot = expectedAnnots.get(annot.label);
+ AssertJUnit.assertTrue("Failed AlignmentAnnotation Test for >>> "
+ annot.label, isAnnotationMatched(expectedAnnot, annot));
passedCount++;
}
- Assert.assertEquals("Some Sequences did not pass the test",
+ 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,
@@ -264,13 +490,14 @@ public class JSONFileTest
+ actualGrp.getStartRes());
System.out.println(expectedGrp.getEndRes() + " | "
+ actualGrp.getEndRes());
+ System.out.println(expectedGrp.cs + " | " + actualGrp.cs);
if (expectedGrp.getName().equals(actualGrp.getName())
&& expectedGrp.getColourText() == actualGrp.getColourText()
&& expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
&& expectedGrp.getIgnoreGapsConsensus() == actualGrp
.getIgnoreGapsConsensus()
- && expectedGrp.cs.equals(actualGrp.cs)
+ && (expectedGrp.cs.getClass().equals(actualGrp.cs.getClass()))
&& expectedGrp.getSequences().size() == actualGrp
.getSequences().size()
&& expectedGrp.getStartRes() == actualGrp.getStartRes()
@@ -338,4 +565,47 @@ public class JSONFileTest
// System.out.println(">>>>>>>>>>>>>> features matched : " + matched);
return matched;
}
+
+ /**
+ * 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(),
+ 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 = expectedGrps.get(seqGrp.getName());
+ 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);
+ }
}