fixing array processing order

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

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index 158c901..2d5f7a2 100644 (file)
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -22,7 +22,8 @@ package jalview.io;
 
 import static org.testng.AssertJUnit.assertNotNull;
 
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
+import jalview.datamodel.AlignExportSettingsAdapter;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -42,6 +43,7 @@ import jalview.schemes.ResidueColourScheme;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -93,7 +95,7 @@ public class JSONFileTest
 
   private JSONFile jf;
 
-  private AlignExportSettingI exportSettings;
+  private AlignExportSettingsI exportSettings;
 
   @BeforeTest(alwaysRun = true)
   public void setup() throws Exception
@@ -205,46 +207,9 @@ public class JSONFileTest
     TEST_SEQ_HEIGHT = expectedSeqs.size();
     TEST_GRP_HEIGHT = expectedGrps.size();
     TEST_ANOT_HEIGHT = expectedAnnots.size();
-    TEST_CS_HEIGHT = expectedColSel.getHiddenColumnsCopy().size();
+    TEST_CS_HEIGHT = expectedColSel.getNumberOfRegions();
 
-    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;
-      }
-    };
+    exportSettings = new AlignExportSettingsAdapter(true);
 
     AppletFormatAdapter formatAdapter = new AppletFormatAdapter();
     try
@@ -271,7 +236,7 @@ public class JSONFileTest
       testAlignment = formatAdapter.readFile(jsonOutput,
               DataSourceType.PASTE, FileFormat.Json);
       testJsonFile = (JSONFile) formatAdapter.getAlignFile();
-      // System.out.println(jsonOutput);
+      System.out.println(jsonOutput);
     } catch (IOException e)
     {
       e.printStackTrace();
@@ -325,11 +290,12 @@ public class JSONFileTest
   {
     HiddenColumns cs = testJsonFile.getHiddenColumns();
     Assert.assertNotNull(cs);
-    Assert.assertNotNull(cs.getHiddenColumnsCopy());
-    List<int[]> hiddenCols = cs.getHiddenColumnsCopy();
-    Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
-    Assert.assertEquals(hiddenCols.get(0), expectedColSel
-            .getHiddenColumnsCopy().get(0),
+
+    Iterator<int[]> it = cs.iterator();
+    Iterator<int[]> colselit = expectedColSel.iterator();
+    Assert.assertTrue(it.hasNext());
+    Assert.assertEquals(cs.getNumberOfRegions(), TEST_CS_HEIGHT);
+    Assert.assertEquals(it.next(), colselit.next(),
             "Mismatched hidden columns!");
   }