JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index 181aabd..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;
 
@@ -29,11 +30,19 @@ 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");
 
@@ -45,16 +54,15 @@ public class TCoffeeScoreFileTest
   {
 
     TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
     AssertJUnit.assertTrue(scoreFile.getWarningMessage(),
             scoreFile.isValid());
 
     Header header = scoreFile.header;
     AssertJUnit.assertNotNull(header);
-    AssertJUnit
-            .assertEquals(
-                    "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
-                    header.head);
+    AssertJUnit.assertEquals(
+            "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
+            header.head);
     AssertJUnit.assertEquals(90, header.score);
     AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
     AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
@@ -73,7 +81,7 @@ public class TCoffeeScoreFileTest
     try
     {
       TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
-              FormatAdapter.FILE);
+              DataSourceType.FILE);
       AssertJUnit.assertFalse(result.isValid());
     } catch (IOException x)
     {
@@ -86,7 +94,7 @@ public class TCoffeeScoreFileTest
   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());
@@ -107,7 +115,7 @@ 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);
@@ -145,44 +153,35 @@ public class TCoffeeScoreFileTest
   {
 
     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
 
-    AssertJUnit
-            .assertEquals(
-                    "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
-                    parser.getScoresFor("1PHT"));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
-                    parser.getScoresFor("1BB9"));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
-                    parser.getScoresFor("1UHC"));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
-                    parser.getScoresFor("1YCS"));
-    AssertJUnit
-            .assertEquals(
-                    "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
-                    parser.getScoresFor("1OOT"));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
-                    parser.getScoresFor("1ABO"));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
-                    parser.getScoresFor("1FYN"));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
-                    parser.getScoresFor("1QCF"));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
-                    parser.getScoresFor("cons"));
+    AssertJUnit.assertEquals(
+            "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
+            parser.getScoresFor("1PHT"));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
+            parser.getScoresFor("1BB9"));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
+            parser.getScoresFor("1UHC"));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
+            parser.getScoresFor("1YCS"));
+    AssertJUnit.assertEquals(
+            "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
+            parser.getScoresFor("1OOT"));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
+            parser.getScoresFor("1ABO"));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
+            parser.getScoresFor("1FYN"));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
+            parser.getScoresFor("1QCF"));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
+            parser.getScoresFor("cons"));
   }
 
   @Test(groups = { "Functional" })
@@ -190,45 +189,36 @@ public class TCoffeeScoreFileTest
   {
 
     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
     List<String> scores = parser.getScoresList();
-    AssertJUnit
-            .assertEquals(
-                    "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
-                    scores.get(0));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
-                    scores.get(1));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
-                    scores.get(2));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
-                    scores.get(3));
-    AssertJUnit
-            .assertEquals(
-                    "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
-                    scores.get(4));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
-                    scores.get(5));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
-                    scores.get(6));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
-                    scores.get(7));
-    AssertJUnit
-            .assertEquals(
-                    "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
-                    scores.get(8));
+    AssertJUnit.assertEquals(
+            "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
+            scores.get(0));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
+            scores.get(1));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
+            scores.get(2));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
+            scores.get(3));
+    AssertJUnit.assertEquals(
+            "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
+            scores.get(4));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
+            scores.get(5));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
+            scores.get(6));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
+            scores.get(7));
+    AssertJUnit.assertEquals(
+            "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
+            scores.get(8));
 
   }
 
@@ -237,7 +227,7 @@ public class TCoffeeScoreFileTest
   {
 
     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
     byte[][] scores = parser.getScoresArray();
 
@@ -267,7 +257,8 @@ public class TCoffeeScoreFileTest
   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());