From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Sat, 17 Nov 2012 21:59:42 +0000 (+0000)
Subject: Merge branch 'develop' into menard
X-Git-Tag: Jalview_2_9~265^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ffacb1793ba68710f95b293a45eb4b0868b722a2;p=jalview.git

Merge branch 'develop' into menard
---

ffacb1793ba68710f95b293a45eb4b0868b722a2
diff --cc src/jalview/io/TCoffeeScoreFile.java
index 178caad,ad5f52a..56994ae
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@@ -30,16 -30,9 +30,18 @@@ import java.util.HashMap
  import java.util.LinkedHashMap;
  import java.util.List;
  import java.util.Map;
+ import java.util.regex.Matcher;
+ import java.util.regex.Pattern;
  
 +import javax.xml.parsers.ParserConfigurationException;
 +
 +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;
 +
  /**
   * A file parse for T-Coffee score ascii format. This file contains the
   * alignment consensus for each resude in any sequence.
diff --cc test/jalview/io/TCoffeeScoreFileTest.java
index 2c09148,3147054..1ee4936
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@@ -21,35 -21,25 +21,33 @@@ 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, 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 );
@@@ -66,11 -56,12 +64,12 @@@
  	
  	
  	@Test
 -	public void testWrongFile() {
 +	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);
  	    }