Merge branch 'develop' into releases/Release_2_11_2_Branch

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

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index c9b5f4a..9c4be2d 100644 (file)
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -20,22 +20,36 @@
  */
 package jalview.io;
 
+import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.io.AnnotationFile.ViewDef;
-
+import java.awt.Color;
 import java.io.File;
 import java.util.Hashtable;
+import java.util.List;
 
 import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.AnnotationFile.ViewDef;
+
 public class AnnotationFileIOTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   static String TestFiles[][] = {
       { "Test example annotation import/export", "examples/uniref50.fa",
           "examples/testdata/example_annot_file.jva" },
@@ -61,7 +75,7 @@ public class AnnotationFileIOTest
     }
   }
 
-  public static AlignmentI readAlignmentFile(File f)
+  protected AlignmentI readAlignmentFile(File f)
   {
     System.out.println("Reading file: " + f);
     String ff = f.getPath();
@@ -69,8 +83,8 @@ public class AnnotationFileIOTest
     {
       FormatAdapter rf = new FormatAdapter();
 
-      AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
-              new IdentifyFile().identify(ff, AppletFormatAdapter.FILE));
+      AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
+              new IdentifyFile().identify(ff, DataSourceType.FILE));
 
       // make sure dataset is initialised ? not sure about this
       for (int i = 0; i < al.getSequencesArray().length; ++i)
@@ -97,9 +111,7 @@ public class AnnotationFileIOTest
    *          - label for IO class used to write and read back in the data from
    *          f
    */
-
-  // @Test(groups ={ "Functional" })
-  public static void testAnnotationFileIO(String testname, File f,
+  void testAnnotationFileIO(String testname, File f,
           File annotFile)
   {
     System.out.println("Test: " + testname + "\nReading annotation file '"
@@ -108,15 +120,16 @@ public class AnnotationFileIOTest
     try
     {
       AlignmentI al = readAlignmentFile(f);
-      ColumnSelection cs = new ColumnSelection();
+      HiddenColumns cs = new HiddenColumns();
       assertTrue(
               "Test "
                       + testname
                       + "\nAlignment was not annotated - annotation file not imported.",
               new AnnotationFile().readAnnotationFile(al, cs, af,
-                      FormatAdapter.FILE));
+                      DataSourceType.FILE));
 
       AnnotationFile aff = new AnnotationFile();
+      // ViewDef is not used by Jalview
       ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
               new Hashtable());
       String anfileout = new AnnotationFile().printAnnotations(
@@ -142,10 +155,11 @@ public class AnnotationFileIOTest
                       + testname
                       + "\nregenerated annotation file did not annotate alignment.",
               new AnnotationFile().readAnnotationFile(al_new, anfileout,
-                      FormatAdapter.PASTE));
+                      DataSourceType.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+              false);
       return;
     } catch (Exception e)
     {
@@ -156,4 +170,45 @@ public class AnnotationFileIOTest
             + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
             + annotFile + "'.");
   }
+  
+  @Test(groups="Functional")
+  public void testAnnotateAlignmentView()
+  {
+    long t1 = System.currentTimeMillis();
+    /*
+     * JAL-3779 test multiple groups of the same name get annotated
+     */
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            ">Seq1\nQRSIL\n>Seq2\nFTHND\n>Seq3\nRPVSL\n",
+            DataSourceType.PASTE);
+    long t2 = System.currentTimeMillis();
+    System.err.println("t0: " + (t2 - t1));
+    // seq1 and seq3 are in distinct groups both named Group1
+    String annotationFile = "JALVIEW_ANNOTATION\nSEQUENCE_GROUP\tGroup1\t*\t*\t1\n"
+            + "SEQUENCE_GROUP\tGroup2\t*\t*\t2\n"
+            + "SEQUENCE_GROUP\tGroup1\t*\t*\t3\n"
+            + "PROPERTIES\tGroup1\toutlineColour=blue\tidColour=red\n";
+    new AnnotationFile().annotateAlignmentView(af.getViewport(), annotationFile, DataSourceType.PASTE);
+    
+    AlignmentI al = af.getViewport().getAlignment();
+    List<SequenceGroup> groups = al.getGroups();
+    assertEquals(3, groups.size());
+    SequenceGroup sg = groups.get(0);
+    assertEquals("Group1", sg.getName());
+    assertTrue(sg.contains(al.getSequenceAt(0)));
+    assertEquals(Color.BLUE, sg.getOutlineColour());
+    assertEquals(Color.RED, sg.getIdColour());
+    sg = groups.get(1);
+    assertEquals("Group2", sg.getName());
+    assertTrue(sg.contains(al.getSequenceAt(1)));
+    
+    /*
+     * the bug fix: a second group of the same name is also given properties
+     */
+    sg = groups.get(2);
+    assertEquals("Group1", sg.getName());
+    assertTrue(sg.contains(al.getSequenceAt(2)));
+    assertEquals(Color.BLUE, sg.getOutlineColour());
+    assertEquals(Color.RED, sg.getIdColour());
+  }
 }