X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fio%2FJSONFileTest.java;h=2aff5ccd88dccc92e1978ac41cf0e54e116a00f8;hb=0125cee3edfa0ba5584631bae3ad9c808ec0b30d;hp=957343bf474f4a44e3381d36e406648b1d344f47;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index 957343b..2aff5cc 100644
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -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;
@@ -90,6 +91,8 @@ public class JSONFileTest
 
   private JSONFile jf;
 
+  private AlignExportSettingI exportSettings;
+
   @BeforeTest(alwaysRun = true)
   public void setup() throws Exception
   {
@@ -127,13 +130,14 @@ public class JSONFileTest
       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<SequenceI>();
     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);
@@ -191,9 +195,9 @@ public class JSONFileTest
     TEST_SEQ_HEIGHT = expectedSeqs.size();
     TEST_GRP_HEIGHT = expectedGrps.size();
     TEST_ANOT_HEIGHT = expectedAnnots.size();
-    TEST_CS_HEIGHT = expectedColSel.getListOfCols().size();
+    TEST_CS_HEIGHT = expectedColSel.getHiddenRegions().size();
 
-    AlignExportSettingI exportSettings = new AlignExportSettingI()
+    exportSettings = new AlignExportSettingI()
     {
       @Override
       public boolean isExportHiddenSequences()
@@ -311,11 +315,11 @@ public class JSONFileTest
   {
     HiddenColumns cs = testJsonFile.getHiddenColumns();
     Assert.assertNotNull(cs);
-    Assert.assertNotNull(cs.getListOfCols());
-    List<int[]> hiddenCols = cs.getListOfCols();
+    Assert.assertNotNull(cs.getHiddenRegions());
+    List<int[]> hiddenCols = cs.getHiddenRegions();
     Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
     Assert.assertEquals(hiddenCols.get(0), expectedColSel
-            .getListOfCols().get(0),
+            .getHiddenRegions().get(0),
             "Mismatched hidden columns!");
   }
 
@@ -337,6 +341,58 @@ public class JSONFileTest
             "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()
   {
@@ -509,4 +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<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 = 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);
+  }
 }