X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=a63923af60ca5cce0188bfb7b5d5a797648a1a82;hb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;hp=7d6a15fcc13eb8bf9f4014bef90fa92bb3a6d404;hpb=ae3a5e9ecc087f6ada0cee07efde4b0d0ba76a41;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 7d6a15f..a63923a 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -1,31 +1,37 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+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.io.File;
+import java.util.Hashtable;
 
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.Test;
 
 public class AnnotationFileIOTest
 {
@@ -42,14 +48,17 @@ public class AnnotationFileIOTest
           "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" } };
+          "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]));
     }
   }
 
@@ -63,11 +72,12 @@ public class AnnotationFileIOTest
 
       AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
               new IdentifyFile().Identify(ff, AppletFormatAdapter.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).setDatasetSequence(
+                al.getSequenceAt(i).createDatasetSequence());
       }
       assertNotNull("Couldn't read supplied alignment data.", al);
       return al;
@@ -75,9 +85,10 @@ 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
@@ -88,32 +99,63 @@ 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)
+
+  // @Test(groups ={ "Functional" })
+  public static 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");
-      
+      ColumnSelection cs = new ColumnSelection();
+      assertTrue(
+              "Test "
+                      + testname
+                      + "\nAlignment was not annotated - annotation file not imported.",
+              new AnnotationFile().readAnnotationFile(al, cs, af,
+                      FormatAdapter.FILE));
+
+      AnnotationFile aff = new AnnotationFile();
+      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,
+                      FormatAdapter.PASTE));
+
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, 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 + "'.");
   }
 }