X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FTCoffeeScoreFileTest.java;h=3b6c30a680e9225581225f6e8e921b593c0077be;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=73084461cd01b3463ca9c33b01d84c44242f5c7e;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index 7308446..3b6c30a 100644
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -21,12 +22,9 @@ import static org.junit.Assert.*;
 import jalview.io.TCoffeeScoreFile.Block;
 import jalview.io.TCoffeeScoreFile.Header;
 
-import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
-import java.io.StringReader;
 import java.util.List;
 
 import org.junit.Test;
@@ -34,14 +32,15 @@ import org.junit.Test;
 public class TCoffeeScoreFileTest {
 
 	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");
+    final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
 	
 	@Test
 	public void testReadHeader() throws IOException, FileNotFoundException {
 
-	        TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
-	        assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
-		Header header = scoreFile.header;
+	    TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
+	    assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
+		
+	    Header header = scoreFile.header;
 		assertNotNull(header);
 		assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
 		assertEquals( 90, header.score );
@@ -60,9 +59,10 @@ public class TCoffeeScoreFileTest {
 	@Test
 	public void testWrongFile() {
 	    try {
-		TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
-		assertFalse(result.isValid());
-	    } catch (IOException x)
+			TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
+			assertFalse(result.isValid());
+	    } 
+	    catch (IOException x)
 	    {
 	      assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
 	    }
@@ -173,6 +173,15 @@ public class TCoffeeScoreFileTest {
 		
 	} 
 	
+	@Test
+	public void testHeightAndWidthWithResidueNumbers() throws IOException {
+		String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
+		TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
+		assertTrue(result.isValid());
+		assertEquals( 5, result.getHeight() );
+		assertEquals( 84, result.getWidth() );
+	} 	
+	
 	
 	
 }