JAL-1432 updated copyright notices

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

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index 85c0bff..3b6c30a 100644 (file)
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -1,15 +1,30 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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 org.junit.Test;
@@ -17,14 +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 );
@@ -43,9 +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);
            }
@@ -156,6 +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() );
+       }       
+       
        
        
 }