Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index b7da5e4..278dd66 100644 (file)
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -20,6 +20,7 @@
  */
 package jalview.io;
 
+import jalview.gui.JvOptionPane;
 import jalview.io.TCoffeeScoreFile.Block;
 import jalview.io.TCoffeeScoreFile.Header;
 
@@ -29,24 +30,33 @@ import java.io.IOException;
 import java.util.List;
 
 import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class TCoffeeScoreFileTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   final static File SCORE_FILE = new File(
           "test/jalview/io/tcoffee.score_ascii");
 
   final static File ALIGN_FILE = new File(
           "test/jalview/io/tcoffee.fasta_aln");
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testReadHeader() throws IOException
   {
 
     TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
-            AppletFormatAdapter.FILE);
-    AssertJUnit.assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid());
+            DataSourceType.FILE);
+    AssertJUnit.assertTrue(scoreFile.getWarningMessage(),
+            scoreFile.isValid());
 
     Header header = scoreFile.header;
     AssertJUnit.assertNotNull(header);
@@ -65,13 +75,13 @@ public class TCoffeeScoreFileTest
     AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testWrongFile()
   {
     try
     {
       TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
-              FormatAdapter.FILE);
+              DataSourceType.FILE);
       AssertJUnit.assertFalse(result.isValid());
     } catch (IOException x)
     {
@@ -80,17 +90,17 @@ public class TCoffeeScoreFileTest
     }
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testHeightAndWidth() throws IOException
   {
     TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     AssertJUnit.assertTrue(result.isValid());
     AssertJUnit.assertEquals(8, result.getHeight());
     AssertJUnit.assertEquals(83, result.getWidth());
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testReadBlock() throws IOException
   {
 
@@ -105,36 +115,45 @@ public class TCoffeeScoreFileTest
             + "1QCF   99999999999999999999999999974-------2---------24\n"
             + "cons   999999999999999999999999999851000110321100001134\n"
             + "\n" + "\n";
-    FileParse source = new FileParse(BLOCK, FormatAdapter.PASTE);
+    FileParse source = new FileParse(BLOCK, DataSourceType.PASTE);
     Block block = TCoffeeScoreFile.readBlock(source, 0);
 
     AssertJUnit.assertNotNull(block);
-    AssertJUnit.assertEquals("999999999999999999999999998762112222543211112134",
+    AssertJUnit.assertEquals(
+            "999999999999999999999999998762112222543211112134",
             block.getScoresFor("1PHT"));
-    AssertJUnit.assertEquals("99999999999999999999999999987-------4322----2234",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999987-------4322----2234",
             block.getScoresFor("1BB9"));
-    AssertJUnit.assertEquals("99999999999999999999999999987-------5321----2246",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999987-------5321----2246",
             block.getScoresFor("1UHC"));
-    AssertJUnit.assertEquals("99999999999999999999999999986-------4321----1-35",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999986-------4321----1-35",
             block.getScoresFor("1YCS"));
-    AssertJUnit.assertEquals("999999999999999999999999999861-------3------1135",
+    AssertJUnit.assertEquals(
+            "999999999999999999999999999861-------3------1135",
             block.getScoresFor("1OOT"));
-    AssertJUnit.assertEquals("99999999999999999999999999986-------422-------34",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999986-------422-------34",
             block.getScoresFor("1ABO"));
-    AssertJUnit.assertEquals("99999999999999999999999999985-------32--------35",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999985-------32--------35",
             block.getScoresFor("1FYN"));
-    AssertJUnit.assertEquals("99999999999999999999999999974-------2---------24",
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999974-------2---------24",
             block.getScoresFor("1QCF"));
-    AssertJUnit.assertEquals("999999999999999999999999999851000110321100001134",
+    AssertJUnit.assertEquals(
+            "999999999999999999999999999851000110321100001134",
             block.getConsensus());
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testParse() throws IOException
   {
 
     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
 
     AssertJUnit.assertEquals(
             "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
@@ -165,12 +184,12 @@ public class TCoffeeScoreFileTest
             parser.getScoresFor("cons"));
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testGetAsList() throws IOException
   {
 
     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
     List<String> scores = parser.getScoresList();
     AssertJUnit.assertEquals(
@@ -203,12 +222,12 @@ public class TCoffeeScoreFileTest
 
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testGetAsArray() throws IOException
   {
 
     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
     byte[][] scores = parser.getScoresArray();
 
@@ -234,11 +253,12 @@ public class TCoffeeScoreFileTest
 
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testHeightAndWidthWithResidueNumbers() throws Exception
   {
     String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
-    TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
+    TCoffeeScoreFile result = new TCoffeeScoreFile(file,
+            DataSourceType.FILE);
     AssertJUnit.assertTrue(result.isValid());
     AssertJUnit.assertEquals(5, result.getHeight());
     AssertJUnit.assertEquals(84, result.getWidth());