X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJSONFileTest.java;h=957343bf474f4a44e3381d36e406648b1d344f47;hb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;hp=da2e64ee4d93b0432f72263fa57586ecd52c826c;hpb=8f118c154e74caaef6bec19acd0466904ac424d4;p=jalview.git

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index da2e64e..957343b 100644
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -27,14 +27,15 @@ 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;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ZappoColourScheme;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -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;
@@ -69,7 +78,7 @@ 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];
 
@@ -114,7 +123,7 @@ public class JSONFileTest
 
     for (Sequence seq : seqs)
     {
-      seq.setDatasetSequence(seq);
+      seq.createDatasetSequence();
       expectedSeqs.put(seq.getName(), seq);
     }
 
@@ -124,9 +133,11 @@ public class JSONFileTest
     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);
+            null, true, true, false, 21, 29);
+    ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
+            "zappo", seqGrp);
+    seqGrp.cs.setColourScheme(scheme);
     seqGrp.setShowNonconserved(false);
     seqGrp.setDescription(null);
 
@@ -180,7 +191,7 @@ 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()
     {
@@ -225,23 +236,26 @@ 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(),
-              jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
+              jf.getHiddenColumns(), AlignFrame.DEFAULT_WIDTH,
               AlignFrame.DEFAULT_HEIGHT);
       af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
-      af.changeColour(jf.getColourScheme());
+      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(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)
@@ -257,7 +271,7 @@ public class JSONFileTest
     passedCount = 0;
   }
 
-  @AfterTest
+  @AfterTest(alwaysRun = true)
   public void tearDown() throws Exception
   {
     testJsonFile = null;
@@ -295,12 +309,13 @@ 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, expectedColSel.getHiddenColumns(),
+    Assert.assertEquals(hiddenCols.get(0), expectedColSel
+            .getListOfCols().get(0),
             "Mismatched hidden columns!");
   }
 
@@ -309,16 +324,16 @@ 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" })
   public void colorSchemeTest()
   {
-    Assert.assertNotNull(testJsonFile.getColourScheme(),
+    Assert.assertNotNull(testJsonFile.getGlobalColourScheme(),
             "Colourscheme is null, parsing failed!");
-    Assert.assertTrue(
-            testJsonFile.getColourScheme() instanceof ZappoColourScheme,
+    Assert.assertEquals(testJsonFile.getGlobalColourScheme(), "Zappo",
             "Zappo colour scheme expected!");
   }
 
@@ -419,13 +434,14 @@ 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()