X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FTCoffeeScoreFileTest.java;h=ce23728062815608b65c6d048e640d6c9e2ea6d3;hb=afd6c9791246b62cdb87cfbac0e9cb31b6c214cf;hp=77ea1fb31dc132df2996da0abb7a1add7c94e6f7;hpb=c5677e9860106a821a3e6e0429b20ede7b9a732a;p=jalview.git

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index 77ea1fb..ce23728 100644
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -1,15 +1,29 @@
+/*
+ * 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;
@@ -20,18 +34,20 @@ 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, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+	public void testReadHeader() throws IOException, FileNotFoundException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
 
-	        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 );
@@ -48,18 +64,19 @@ public class TCoffeeScoreFileTest {
 	
 	
 	@Test
-	public void testWrongFile() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+	public void testWrongFile() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
 	    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);
 	    }
 	} 
 
 	@Test
-	public void testHeightAndWidth() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+	public void testHeightAndWidth() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
 		TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
 		assertTrue(result.isValid());
 		assertEquals( 8, result.getHeight() );
@@ -99,7 +116,7 @@ public class TCoffeeScoreFileTest {
 	}
 
 	@Test
-	public void testParse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+	public void testParse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
 
 		TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
 
@@ -116,7 +133,7 @@ public class TCoffeeScoreFileTest {
 
 	
 	@Test
-	public void testGetAsList() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+	public void testGetAsList() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
 		
           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
           assertTrue(parser.getWarningMessage(),parser.isValid());
@@ -135,7 +152,7 @@ public class TCoffeeScoreFileTest {
 	
 	
 	@Test
-	public void testGetAsArray() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException {
+	public void testGetAsArray() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
 		
           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
           assertTrue(parser.getWarningMessage(),parser.isValid());
@@ -163,6 +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() );
+	} 	
+	
 	
 	
 }