Merge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges

[jalview.git] / test / jalview / io / JSONFileTest.java

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index a8611cc..81d0ef7 100644 (file)
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -27,7 +27,7 @@ import jalview.datamodel.Alignment;
 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;
@@ -36,6 +36,7 @@ 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;
@@ -78,7 +79,7 @@ public class JSONFileTest
 
   private HashMap<String, SequenceGroup> expectedGrps = new HashMap<String, SequenceGroup>();
 
-  private ColumnSelection expectedColSel = new ColumnSelection();
+  private HiddenColumns expectedColSel = new HiddenColumns();
 
   private SequenceI[] expectedHiddenSeqs = new SequenceI[1];
 
@@ -90,6 +91,8 @@ public class JSONFileTest
 
   private JSONFile jf;
 
+  private AlignExportSettingI exportSettings;
+
   @BeforeTest(alwaysRun = true)
   public void setup() throws Exception
   {
@@ -191,9 +194,9 @@ public class JSONFileTest
     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.getListOfCols().size();
 
-    AlignExportSettingI exportSettings = new AlignExportSettingI()
+    exportSettings = new AlignExportSettingI()
     {
       @Override
       public boolean isExportHiddenSequences()
@@ -240,7 +243,7 @@ public class JSONFileTest
       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();
@@ -309,13 +312,13 @@ public class JSONFileTest
   @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.getListOfCols());
+    List<int[]> hiddenCols = cs.getListOfCols();
     Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
     Assert.assertEquals(hiddenCols.get(0), expectedColSel
-            .getHiddenColumns().get(0),
+            .getListOfCols().get(0),
             "Mismatched hidden columns!");
   }
 
@@ -338,6 +341,50 @@ public class JSONFileTest
   }
 
   @Test(groups = { "Functional" })
+  /**
+   * Test for bug JAL-2489, NPE when exporting BioJSON with global colour scheme set as 'None'
+   */
+  public void testBioJSONRoundTripWithGlobalColourSchemeSetAsNone()
+  {
+    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);
+      // Change colour scheme to 'None' and perform round trip
+      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()
   {
     Assert.assertTrue(testJsonFile.isShowSeqFeatures(),