X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=de78aa1e871a7645425962d9ffd53187e2894265;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=64ca141039611bcd32ee2102d02937aa9d502a56;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 64ca141..de78aa1 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,42 +20,60 @@
  */
 package jalview.io;
 
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import jalview.datamodel.AlignmentI;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
 
+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 org.junit.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
 {
 
-  static String TestFiles[][] =
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
   {
-      { "Test example annotation import/export", "examples/uniref50.fa",
-          "examples/testdata/example_annot_file.jva" },
+    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" },
       { "Test multiple combine annotation statements import/export",
           "examples/uniref50.fa",
           "examples/testdata/test_combine_annot.jva" },
-      {
-          "Test multiple combine annotation statements with sequence_ref import/export",
+      { "Test multiple combine annotation statements with sequence_ref import/export",
           "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
-      {
-          "Test group only annotation file parsing results in parser indicating annotation was parsed",
-          "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" } };
+      { "Test group only annotation file parsing results in parser indicating annotation was parsed",
+          "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
+      { "Test hiding/showing of insertions on sequence_ref",
+          "examples/uniref50.fa",
+          "examples/testdata/uniref50_seqref.jva" } };
 
-  @Test
+  @Test(groups = { "Functional" })
   public void exampleAnnotationFileIO() throws Exception
   {
-    for (String[] testPair:TestFiles)
+    for (String[] testPair : TestFiles)
     {
-      testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(testPair[2]));
+      testAnnotationFileIO(testPair[0], new File(testPair[1]),
+              new File(testPair[2]));
     }
   }
 
-  public static AlignmentI readAlignmentFile(File f)
+  protected AlignmentI readAlignmentFile(File f)
   {
     System.out.println("Reading file: " + f);
     String ff = f.getPath();
@@ -63,13 +81,13 @@ 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)
       {
-        al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i).createDatasetSequence());
+        al.getSequenceAt(i).createDatasetSequence();
       }
       assertNotNull("Couldn't read supplied alignment data.", al);
       return al;
@@ -77,9 +95,11 @@ public class AnnotationFileIOTest
     {
       e.printStackTrace();
     }
-    fail("Couln't read the alignment in file '"+f.toString()+"'");
+    Assert.fail(
+            "Couln't read the alignment in file '" + f.toString() + "'");
     return null;
   }
+
   /**
    * test alignment data in given file can be imported, exported and reimported
    * with no dataloss
@@ -90,32 +110,95 @@ public class AnnotationFileIOTest
    *          - label for IO class used to write and read back in the data from
    *          f
    */
-  public static void testAnnotationFileIO(String testname, File f, File annotFile)
+  void testAnnotationFileIO(String testname, File f, File annotFile)
   {
-    System.out.println("Test: "+testname+"\nReading annotation file '"+annotFile+"' onto : " + f);
+    System.out.println("Test: " + testname + "\nReading annotation file '"
+            + annotFile + "' onto : " + f);
     String af = annotFile.getPath();
     try
     {
       AlignmentI al = readAlignmentFile(f);
-      
-      assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE));
-      
-      String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties());
-      assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Null string",anfileout!=null);
-      assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Empty string",anfileout.length()>"JALVIEW_ANNOTATION".length());
-
-      System.out.println("Output annotation file:\n"+anfileout+"\n<<EOF\n");
-      
+      HiddenColumns cs = new HiddenColumns();
+      assertTrue("Test " + testname
+              + "\nAlignment was not annotated - annotation file not imported.",
+              new AnnotationFile().readAnnotationFile(al, cs, af,
+                      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(
+              al.getAlignmentAnnotation(), al.getGroups(),
+              al.getProperties(), null, al, v);
+      assertTrue("Test " + testname
+              + "\nAlignment annotation file was not regenerated. Null string",
+              anfileout != null);
+      assertTrue("Test " + testname
+              + "\nAlignment annotation file was not regenerated. Empty string",
+              anfileout.length() > "JALVIEW_ANNOTATION".length());
+
+      System.out.println(
+              "Output annotation file:\n" + anfileout + "\n<<EOF\n");
+
       AlignmentI al_new = readAlignmentFile(f);
-      assertTrue("Test "+testname+"\nregenerated annotation file did not annotate alignment.",new AnnotationFile().readAnnotationFile(al_new, anfileout, FormatAdapter.PASTE));
-      
+      assertTrue("Test " + testname
+              + "\nregenerated annotation file did not annotate alignment.",
+              new AnnotationFile().readAnnotationFile(al_new, anfileout,
+                      DataSourceType.PASTE));
+
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+              false);
       return;
     } catch (Exception e)
     {
       e.printStackTrace();
     }
-    fail("Test "+testname+"\nCouldn't complete Annotation file roundtrip input/output/input test for '"+annotFile+"'.");
+    Assert.fail("Test " + testname
+            + "\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());
   }
 }