X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FTCoffeeScoreFileTest.java;h=85c0bff282a40cedc3014f3acb7b02c14dafd449;hb=1c66dc9053356a709e9cd9d3282517b5221f1ba2;hp=7257e144fd762488ed14ec25706c28721afc5af1;hpb=ef23315db576f5451de0fcb850f645c5db222b20;p=jalview.git

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index 7257e14..85c0bff 100644
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -16,12 +16,15 @@ import org.junit.Test;
 
 public class TCoffeeScoreFileTest {
 
-	final static File SCORE_FILE = new File("./test/jalview/io/tcoffee.score_ascii");
+	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");
 	
 	@Test
-	public void testReadHeader() throws FileNotFoundException {
+	public void testReadHeader() throws IOException, FileNotFoundException {
 
-		Header header = TCoffeeScoreFile.readHeader( new BufferedReader(new FileReader(SCORE_FILE)) );
+	        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 );
@@ -39,14 +42,19 @@ public class TCoffeeScoreFileTest {
 	
 	@Test
 	public void testWrongFile() {
-		TCoffeeScoreFile result = TCoffeeScoreFile.load(new File("./test/jalview/io/tcoffee.fasta_aln"));
-		assertNull(result);
+	    try {
+		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() {
-		TCoffeeScoreFile result = TCoffeeScoreFile.load(new File("./test/jalview/io/tcoffee.score_ascii"));
-		assertNotNull(result);
+	public void testHeightAndWidth() throws IOException {
+		TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
+		assertTrue(result.isValid());
 		assertEquals( 8, result.getHeight() );
 		assertEquals( 83, result.getWidth() );
 	} 	
@@ -68,9 +76,10 @@ public class TCoffeeScoreFileTest {
 				"cons   999999999999999999999999999851000110321100001134\n" +
 				"\n" +
 				"\n";
-		
-		Block block = TCoffeeScoreFile.readBlock(new BufferedReader(new StringReader(BLOCK)), 0);
-		assertNotNull(block);
+		FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
+		Block block = TCoffeeScoreFile.readBlock(source, 0);
+
+                assertNotNull(block);
 		assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
 		assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
 		assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
@@ -83,9 +92,9 @@ public class TCoffeeScoreFileTest {
 	}
 
 	@Test
-	public void testParse() throws FileNotFoundException {
+	public void testParse() throws IOException {
 
-		TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
+		TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
 
 		assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
 		assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
@@ -100,10 +109,10 @@ public class TCoffeeScoreFileTest {
 
 	
 	@Test
-	public void testGetAsList() throws FileNotFoundException {
+	public void testGetAsList() throws IOException {
 		
-		TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
-
+          TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
+          assertTrue(parser.getWarningMessage(),parser.isValid());
 		List<String> scores = parser.getScoresList();
 		assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
 		assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
@@ -119,10 +128,10 @@ public class TCoffeeScoreFileTest {
 	
 	
 	@Test
-	public void testGetAsArray() throws FileNotFoundException {
+	public void testGetAsArray() throws IOException {
 		
-		TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
-
+          TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
+          assertTrue(parser.getWarningMessage(),parser.isValid());
 		byte[][] scores = parser.getScoresArray();
 	
 		assertEquals( 9, scores[0][0] );