X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FTCoffeeScoreFileTest.java;h=6d11ebed96e5bb5db5605a29337769e3ad616b01;hb=80c223c45fde0899c9794e887801dd82fffd3452;hp=85c0bff282a40cedc3014f3acb7b02c14dafd449;hpb=1c66dc9053356a709e9cd9d3282517b5221f1ba2;p=jalview.git

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index 85c0bff..6d11ebe 100644
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -1,30 +1,53 @@
+/*
+ * 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
+ * 
+ * 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.
+ *  
+ * 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/>.
+ */
 package jalview.io;
 
 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 javax.xml.parsers.ParserConfigurationException;
+
 import org.junit.Test;
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 
 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 {
+	public void testReadHeader() throws IOException {
 
-	        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 );
@@ -41,11 +64,12 @@ public class TCoffeeScoreFileTest {
 	
 	
 	@Test
-	public void testWrongFile() {
+	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);
 	    }
@@ -156,6 +180,15 @@ public class TCoffeeScoreFileTest {
 		
 	} 
 	
+	@Test
+	public void testHeightAndWidthWithResidueNumbers() throws Exception {
+		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() );
+	} 	
+	
 	
 	
 }