Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index f75f433..a8611cc 100644 (file)
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -33,6 +33,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 
@@ -44,6 +45,7 @@ import java.util.List;
 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;
@@ -51,6 +53,13 @@ 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;
@@ -128,7 +137,7 @@ public class JSONFileTest
             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);
 
@@ -227,7 +236,7 @@ public class JSONFileTest
     try
     {
       alignment = (Alignment) formatAdapter.readFile(TEST_JSON_FILE,
-              AppletFormatAdapter.FILE, JSONFile.FILE_DESC);
+              DataSourceType.FILE, FileFormat.Json);
       jf = (JSONFile) formatAdapter.getAlignFile();
 
       AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(),
@@ -241,12 +250,12 @@ public class JSONFileTest
       af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
 
       formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
-      String jsonOutput = formatAdapter.formatSequences(JSONFile.FILE_DESC,
+      String jsonOutput = formatAdapter.formatSequences(FileFormat.Json,
               af.alignPanel.getAlignment(), false);
 
       formatAdapter = new AppletFormatAdapter();
       testAlignment = formatAdapter.readFile(jsonOutput,
-              AppletFormatAdapter.PASTE, JSONFile.FILE_DESC);
+              DataSourceType.PASTE, FileFormat.Json);
       testJsonFile = (JSONFile) formatAdapter.getAlignFile();
       // System.out.println(jsonOutput);
     } catch (IOException e)
@@ -305,7 +314,8 @@ public class JSONFileTest
     Assert.assertNotNull(cs.getHiddenColumns());
     List<int[]> hiddenCols = cs.getHiddenColumns();
     Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
-    Assert.assertEquals(hiddenCols, expectedColSel.getHiddenColumns(),
+    Assert.assertEquals(hiddenCols.get(0), expectedColSel
+            .getHiddenColumns().get(0),
             "Mismatched hidden columns!");
   }
 
@@ -314,7 +324,8 @@ public class JSONFileTest
   {
     Assert.assertNotNull(testJsonFile.getHiddenSequences(),
             "Hidden sequence Expected but found Null");
-    Assert.assertEquals(jf.getHiddenSequences().length, 1, "Hidden sequece");
+    Assert.assertEquals(jf.getHiddenSequences().length, 1,
+            "Hidden sequence");
   }
 
   @Test(groups = { "Functional" })